Composition, splice variants and methods relating to ovarian specific genes and proteins

ABSTRACT

The present invention relates to newly identified nucleic acid molecules and polypeptides present in normal and neoplastic ovarian cells, including fragments, variants and derivatives of the nucleic acids and polypeptides. The present invention also relates to antibodies to the polypeptides of the invention, as well as agonists and antagonists of the polypeptides of the invention. The invention also relates to compositions containing the nucleic acid molecules, polypeptides, antibodies, agonists and antagonists of the invention and methods for the use of these compositions. These uses include identifying, diagnosing, monitoring, staging, imaging and treating ovarian cancer and non-cancerous disease states in ovarian, identifying ovarian tissue, monitoring and identifying and/or designing agonists and antagonists of polypeptides of the invention. The uses also include gene therapy, production of transgenic animals and cells, and production of engineered ovarian tissue for treatment and research.

INTRODUCTION

This application claims the benefit of priority from U.S. ProvisionalPatent Application Ser. No. 60/431,321 filed Dec. 6, 2002, U.S.Provisional Patent Application Ser. No. 60/431,301 filed Dec. 6, 2002,U.S. Provisional Patent Application Ser. No. 60/484,584 filed Jun. 30,2003 and U.S. Provisional Patent Application Ser. No. 60/518,607, filedNov. 7, 2003 which are herein incorporated by reference in theirentireties.

FIELD OF THE INVENTION

The present invention relates to newly identified nucleic acids andpolypeptides present in normal and neoplastic ovarian cells, includingfragments, variants and derivatives of the nucleic acids andpolypeptides. The present invention also relates to antibodies to thepolypeptides of the invention, as well as agonists and antagonists ofthe polypeptides of the invention. The invention also relates tocompositions comprising the nucleic acids, polypeptides, antibodies,post translational modifications (PTMs), variants, derivatives, agonistsand antagonists thereto and methods for the use of these compositions.These uses include identifying, diagnosing, monitoring, staging, imagingand treating ovarian cancer and/or non-cancerous disease states inovarian, identifying ovarian tissue and monitoring and identifyingand/or designing agonists and antagonists of polypeptides of theinvention. The uses also include gene therapy, therapeutic moleculesincluding but not limited to antibodies or antisense molecules,production of transgenic animals and cells, and production of engineeredovarian tissue for treatment and research.

BACKGROUND OF THE INVENTION

Cancer of the ovaries is the fourth-most common cause of cancer death inwomen in the United States, with more than 23,000 new cases and roughly14,000 deaths predicted for the year 2001. Shridhar, V. et al., CancerRes. 61(15):5895-904 (2001); Memarzadeh, S. & Berek, J. S., J. Reprod.Med. 46(7):621-29 (2001). The incidence of ovarian cancer is of seriousconcern worldwide, with an estimated 191,000 new cases predictedannually. Runnebaum, I. B. & Stickeler, E., J. Cancer Res. Clin. Oncol.127(2):73-79 (2001). These numbers continue to rise today. In the UnitedStates alone, it is estimated there will be 25,400 new cases of ovariancancer, and 14,300 deaths due to ovarian cancer in 2003. (AmericanCancer Society Website: cancer.org on the world wide web).Unfortunately, women with ovarian cancer are typically asymptomaticuntil the disease has metastasized. Because effective screening forovarian cancer is not available, roughly 70% of women diagnosed have anadvanced stage of the cancer with a five-year survival rate of ˜25-30%.Memarzadeh, S. & Berek, J. S., supra; Nunns, D. et al, Obstet. Gynecol.Surv. 55(12):746-51. Conversely, women diagnosed with early stageovarian cancer enjoy considerably higher survival rates. Werness, B. A.& Eltabbakh, G. H., Int'l. J. Gynecol. Pathol. 20(1):48-63 (2001).Although our understanding of the etiology of ovarian cancer isincomplete, the results of extensive research in this area point to acombination of age, genetics, reproductive, and dietary/environmentalfactors. Age is a key risk factor in the development of ovarian cancer:while the risk for developing ovarian cancer before the age of 30 isslim, the incidence of ovarian cancer rises linearly between ages 30 to50, increasing at a slower rate thereafter, with the highest incidencebeing among septagenarian women. Jeanne M. Schilder et al., HereditaryOvarian Cancer: Clinical Syndromes and Management, in Ovarian Cancer 182(Stephen C. Rubin & Gregory P. Sutton eds., 2d ed. 2001).

With respect to genetic factors, a family history of ovarian cancer isthe most significant risk factor in the development of the disease, withthat risk depending on the number of affected family members, the degreeof their relationship to the woman, and which particular first degreerelatives are affected by the disease. Id. Mutations in several geneshave been associated with ovarian cancer, including BRCA1 and BRCA2,both of which play a key role in the development of breast cancer, aswell as hMSH2 and hMLH1, both of which are associated with hereditarynon-polyposis colon cancer. Katherine Y. Look, Epidemiology, Etiology,and Screening of Ovarian Cancer, in Ovarian Cancer 169, 171-73 (StephenC. Rubin & Gregory P. Sutton eds., 2d ed. 2001). BRCA1, located onchromosome 17, and BRCA2, located on chromosome 13, are tumor suppressorgenes implicated in DNA repair; mutations in these genes are linked toroughly 10% of ovarian cancers. Id. at 171-72; Schilder et al., supra at185-86. hMSH2 and hMLH1 are associated with DNA mismatch repair, and arelocated on chromosomes 2 and 3, respectively; it has been reported thatroughly 3% of hereditary ovarian carcinomas are due to mutations inthese genes. Look, supra at 173; Schilder et al., supra at 184, 188-89.

Reproductive factors have also been associated with an increased orreduced risk of ovarian cancer. Late menopause, nulliparity, and earlyage at menarche have all been linked with an elevated risk of ovariancancer. Schilder et al., supra at 182. One theory hypothesizes thatthese factors increase the number of ovulatory cycles over the course ofa woman's life, leading to “incessant ovulation,” which is thought to bethe primary cause of mutations to the ovarian epithelium. Id; Laura J.Havrilesky & Andrew Berchuck, Molecular Alterations in Sporadic OvarianCancer, in Ovarian Cancer 25 (Stephen C. Rubin & Gregory P. Sutton eds.,2d ed. 2001). The mutations may be explained by the fact that ovulationresults in the destruction and repair of that epithelium, necessitatingincreased cell division, thereby increasing the possibility that anundetected mutation will occur. Id. Support for this theory may be foundin the fact that pregnancy, lactation, and the use of oralcontraceptives, all of which suppress ovulation, confer a protectiveeffect with respect to developing ovarian cancer. Id.

Among dietary/environmental factors, there would appear to be anassociation between high intake of animal fat or red meat and ovariancancer, while the antioxidant Vitamin A, which prevents free radicalformation and also assists in maintaining normal cellulardifferentiation, may offer a protective effect. Look, supra at 169.Reports have also associated asbestos and hydrous magnesium trisilicate(talc), the latter of which may be present in diaphragms and sanitarynapkins. Id. at 169-70.

Current screening procedures for ovarian cancer, while of some utility,are quite limited in their diagnostic ability, a problem that isparticularly acute at early stages of cancer progression when thedisease is typically asymptomatic yet is most readily treatable. WalterJ. Burdette, Cancer: Etiology, Diagnosis, and Treatment 166 (1998);Memarzadeh & Berek, supra; Runnebaum & Stickeler, supra; Werness &Eltabbakh, supra. Commonly used screening tests include biannualrectovaginal pelvic examination, radioimmunoassay to detect the CA-125serum tumor marker, and transvaginal ultrasonography. Burdette, supra at166.

Pelvic examination has failed to yield adequate numbers of earlydiagnoses, and the other methods are not sufficiently accurate. Id. Onestudy reported that only 15% of patients who suffered from ovariancancer were diagnosed with the disease at the time of their pelvicexamination. Look, supra at 174. Moreover, the CA-125 test is prone togiving false positives in pre-menopausal women and has been reported tobe of low predictive value in post-menopausal women. Id. at 174-75.Although transvaginal ultrasonography is now the preferred procedure forscreening for ovarian cancer, it is unable to distinguish reliablybetween benign and malignant tumors, and also cannot locate primaryperitoneal malignancies or ovarian cancer if the ovary size is normal.Schilder et al., supra at 194-95. While genetic testing for mutations ofthe BRCA1, BRCA2, hMSH2, and hMLH1 genes is now available, these testsmay be too costly for some patients and may also yield false negative orindeterminate results. Schilder et al., supra at 191-94.

The staging of ovarian cancer, which is accomplished through surgicalexploration, is crucial in determining the course of treatment andmanagement of the disease. AJCC Cancer Staging Handbook 187 (Irvin D.Fleming et al. eds., 5th ed. 1998); Burdette, supra at 170; Memarzadeh &Berek, supra; Shridhar et al., supra. Staging is performed by referenceto the classification system developed by the International Federationof Gynecology and Obstetrics. David H. Moore, Primary SurgicalManagement of Early Epithelial Ovarian Carcinoma, in Ovarian Cancer 203(Stephen C. Rubin & Gregory P. Sutton eds., 2d ed. 2001); Fleming et al.eds., supra at 188. Stage I ovarian cancer is characterized by tumorgrowth that is limited to the ovaries and is comprised of threesubstages. Id. In substage IA, tumor growth is limited to one ovary,there is no tumor on the external surface of the ovary, the ovariancapsule is intact, and no malignant cells are present in ascites orperitoneal washings. Id. Substage IB is identical to A1, except thattumor growth is limited to both ovaries. Id. Substage IC refers to thepresence of tumor growth limited to one or both ovaries, and alsoincludes one or more of the following characteristics: capsule rupture,tumor growth on the surface of one or both ovaries, and malignant cellspresent in ascites or peritoneal washings. Id.

Stage II ovarian cancer refers to tumor growth involving one or bothovaries, along with pelvic extension. Id. Substage IIA involvesextension and/or implants on the uterus and/or fallopian tubes, with nomalignant cells in the ascites or peritoneal washings, while substageIIB involves extension into other pelvic organs and tissues, again withno malignant cells in the ascites or peritoneal washings. Id. SubstageIIC involves pelvic extension as in IIA or IIB, but with malignant cellsin the ascites or peritoneal washings. Id.

Stage III ovarian cancer involves tumor growth in one or both ovaries,with peritoneal metastasis beyond the pelvis confirmed by microscopeand/or metastasis in the regional lymph nodes. Id. Substage IIIA ischaracterized by microscopic peritoneal metastasis outside the pelvis,with substage IIIB involving macroscopic peritoneal metastasis outsidethe pelvis 2 cm or less in greatest dimension. Id. Substage IIIC isidentical to IIIB, except that the metastasis is greater than 2 cm ingreatest dimension and may include regional lymph node metastasis. Id.Lastly, Stage IV refers to the presence distant metastasis, excludingperitoneal metastasis. Id.

While surgical staging is currently the benchmark for assessing themanagement and treatment of ovarian cancer, it suffers from considerabledrawbacks, including the invasiveness of the procedure, the potentialfor complications, as well as the potential for inaccuracy. Moore, supraat 206-208, 213. In view of these limitations, attention has turned todeveloping alternative staging methodologies through understandingdifferential gene expression in various stages of ovarian cancer and byobtaining various biomarkers to help better assess the progression ofthe disease. Vartiainen, J. et al., Int'l J. Cancer, 95(5):313-16(2001); Shridhar et al. supra; Baekelandt, M. et al., J. Clin. Oncol.18(22):3775-81.

The treatment of ovarian cancer typically involves a multiprong attack,with surgical intervention serving as the foundation of treatment.Dennis S. Chi & William J. Hoskins, Primary Surgical Management ofAdvanced Epithelial Ovarian Cancer, in Ovarian Cancer 241 (Stephen C.Rubin & Gregory P. Sutton eds., 2d ed. 2001). For example, in the caseof epithelial ovarian cancer, which accounts for ˜90% of cases ofovarian cancer, treatment typically consists of: (1) cytoreductivesurgery, including total abdominal hysterectomy, bilateralsalpingo-oophorectomy, omentectomy, and lymphadenectomy, followed by (2)adjuvant chemotherapy with paclitaxel and either cisplatin orcarboplatin. Eltabbakh, G. H. & Awtrey, C. S., Expert Op. Pharmacother.2(10):109-24. Despite a clinical response rate of 80% to the adjuvanttherapy, most patients experience tumor recurrence within three years oftreatment. Id. Certain patients may undergo a second cytoreductivesurgery and/or second-line chemotherapy. Memarzadeh & Berek, supra.

From the foregoing, it is clear that procedures used for detecting,diagnosing, monitoring, staging, prognosticating, and preventing therecurrence of ovarian cancer are of critical importance to the outcomeof the patient Moreover, current procedures, while helpful in each ofthese analyses, are limited by their specificity, sensitivity,invasiveness, and/or their cost. As such, highly specific and sensitiveprocedures that would operate by way of detecting novel markers incells, tissues, or bodily fluids, with minimal invasiveness and at areasonable cost, would be highly desirable.

Breast cancer, also referred to as mammary tumor cancer, is the secondmost common cancer among women, accounting for a third of the cancersdiagnosed in the United States. One in nine women will develop breastcancer in her lifetime and about 192,000 new cases of breast cancer arediagnosed annually with about 42,000 deaths. Bevers, Primary Preventionof Breast Cancer, in Breast Cancer. 20-54 (Kelly K Hunt et al., ed.,2001); Kochanek et al., 49 Nat'l. Vital Statistics Reports 1, 14 (2001).Breast cancer is extremely rare in women younger than 20 and is veryrare in women under 30. The incidence of breast cancer rises with ageand becomes significant by age 50. White Non-Hispanic women have thehighest incidence rate for breast cancer and Korean women have thelowest. Increased prevalence of the genetic mutations BRCA1 and BRCA2that promote breast and other cancers are found in Ashkenazi Jews.African American women have the highest mortality rate for breast canceramong these same groups (31 per 100,000), while Chinese women have thelowest at 11 per 100,000. Although men can get breast cancer, this isextremely rare. In the United States it is estimated there will be212,600 new cases of breast cancer and 40,200 deaths due to breastcancer in 2003. (American Cancer Society Website: cancer.org on theworld wide web). With the exception of those cases with associatedgenetic factors, precise causes of breast cancer are not known.

In the treatment of breast cancer, there is considerable emphasis ondetection and risk assessment because early and accurate staging ofbreast cancer has a significant impact on survival. For example, breastcancer detected at an early stage (stage T0, discussed below) has afive-year survival rate of 92%. Conversely, if the cancer is notdetected until a late stage (i.e., stage T4 (IV)), the five-yearsurvival rate is reduced to 13%. AJCC Cancer Staging Handbook pp. 164-65(Irvin D. Fleming et al. eds., 5^(th) ed. 1998). Some detectiontechniques, such as mammography and biopsy, involve increaseddiscomfort, expense, and/or radiation, and are only prescribed only topatients with an increased risk of breast cancer.

Current methods for predicting or detecting breast cancer risk are notoptimal. One method for predicting the relative risk of breast cancer isby examining a patient's risk factors and pursuing aggressive diagnosticand treatment regiments for high risk patients. A patient's risk ofbreast cancer has been positively associated with increasing age,nulliparity, family history of breast cancer, personal history of breastcancer, early menarche, late menopause, late age of first full termpregnancy, prior proliferative breast disease, irradiation of the breastat an early age and a personal history of malignancy. Lifestyle factorssuch as fat consumption, alcohol consumption, education, andsocioeconomic status have also been associated with an increasedincidence of breast cancer although a direct cause and effectrelationship has not been established. While these risk factors arestatistically significant, their weak association with breast cancerlimited their usefulness. Most women who develop breast cancer have noneof the risk factors listed above, other than the risk that comes withgrowing older. NIH Publication No. 00-1556 (2000).

Current screening methods for detecting cancer, such as breast selfexam, ultrasound, and mammography have drawbacks that reduce theireffectiveness or prevent their widespread adoption. Breast self exams,while useful, are unreliable for the detection of breast cancer in theinitial stages where the tumor is small and difficult to detect bypalpation. Ultrasound measurements require skilled operators at anincreased expense. Mammography, while sensitive, is subject to overdiagnosis in the detection of lesions that have questionable malignantpotential. There is also the fear of the radiation used in mammographybecause prior chest radiation is a factor associated with an increaseincidence of breast cancer.

At this time, there are no adequate methods of breast cancer prevention.The current methods of breast cancer prevention involve prophylacticmastectomy (mastectomy performed before cancer diagnosis) andchemoprevention (chemotherapy before cancer diagnosis) which are drasticmeasures that limit their adoption even among women with increased riskof breast cancer. Bevers, supra.

A number of genetic markers have been associated with breast cancer.Examples of these markers include carcinoembryonic antigen (CEA) (Mughalet al., JAMA 249:1881 (1983)), MUC-1 (Frische and Liu, J. Clin. Ligand22:320 (2000)), HER-2/neu (Haris et al., Proc. Am. Soc. Clin. Oncology15:A96 (1996)), uPA, PAI-1, LPA, LPC, RAK and BRCA (Esteva and Fritsche,Serum and Tissue Markers for Breast Cancer, in Breast Cancer, 286-308(2001)). These markers have problems with limited sensitivity, lowcorrelation, and false negatives which limit their use for initialdiagnosis. For example, while the BRCA1 gene mutation is useful as anindicator of an increased risk for breast cancer, it has limited use incancer diagnosis because only 6.2% of breast cancers are BRCA1 positive.Malone et al., JAMA 279:922 (1998). See also, Mewman et al., JAMA279:915 (1998) (correlation of only 3.3%).

There are four primary classifications of breast cancer varying by thesite of origin and the extent of disease development.

-   -   I. Ductal carcinoma in situ (DCIS): Malignant transformation of        ductal epithelial cells that remain in their normal position.        DCIS is a purely localized disease, incapable of metastasis.    -   II. Invasive ductal carcinoma (IDC): Malignancy of the ductal        epithelial cells breaking through the basal membrane and into        the supporting tissue of the breast. IDC may eventually spread        elsewhere in the body.    -   III. Lobular carcinoma in situ (LCIS): Malignancy arising in a        single lobule of the breast that fail to extend through the        lobule wall, it generally remains localized.    -   IV. Infiltrating lobular carcinoma (ILC): Malignancy arising in        a single lobule of the breast and invading directly through the        lobule wall into adjacent tissues. By virtue of its invasion        beyond the lobule wall, ILC may penetrate lymphatics and blood        vessels and spread to distant sites.

For purpose of determining prognosis and treatment, these four breastcancer types have been staged according to the size of the primary tumor(T), the involvement of lymph nodes (N), and the presence of metastasis(M). Although DCIS by definition represents localized stage I disease,the other forms of breast cancer may range from stage II to stage IV.There are additional prognostic factors that further serve to guidesurgical and medical intervention. The most common ones are total numberof lymph nodes involved, ER (estrogen receptor) status, Her2/neureceptor status and histologic grades.

Breast cancers are diagnosed into the appropriate stage categoriesrecognizing that different treatments are more effective for differentstages of cancer. Stage TX indicates that primary tumor cannot beassessed (i.e., tumor was removed or breast tissue was removed). StageT0 is characterized by abnormalities such as hyperplasia but with noevidence of primary tumor. Stage Tis is characterized by carcinoma insitu, intraductal carcinoma, lobular carcinoma in situ, or Paget'sdisease of the nipple with no tumor. Stage T1 (I) is characterized ashaving a tumor of 2 cm or less in the greatest dimension. Within stageT1, Tmic indicates microinvasion of 0.1 cm or less, T1a indicates atumor of between 0.1 to 0.5 cm, T1b indicates a tumor of between 0.5 to1 cm, and T1c indicates tumors of between 1 cm to 2 cm. Stage 12 (II) ischaracterized by tumors from 2 cm to 5 cm in the greatest dimension.Tumors greater than 5 cm in size are classified as stage T3 (III). StageT4 (IV) indicates a tumor of any size with extension to the chest wallor skin. Within stage T4, T4a indicates extension of the tumor to thechest wall, T4b indicates edema or ulceration of the skin of the breastor satellite skin nodules confined to the same breast, T4c indicates acombination of T4a and T4b, and T4d indicates inflammatory carcinoma.AJCC Cancer Staging Handbook pp. 159-70 (Irvin D. Fleming et al. eds.,5^(th) ed. 1998). In addition to standard staging, breast tumors may beclassified according to their estrogen receptor and progesteronereceptor protein status. Fisher et al., Breast Cancer Research andTreatment 7:147 (1986). Additional pathological status, such as HER2/neustatus may also be useful. Thor et al., J. Nat'l. Cancer Inst. 90:1346(1998); Paik et al., J. Nat'l. Cancer Inst. 90:1361 (1998); Hutchins etal., Proc. Am. Soc. Clin. Oncology 17:A2 (1998).; and Simpson et al., J.Clin. Oncology 18:2059 (2000).

In addition to the staging of the primary tumor, breast cancermetastases to regional lymph nodes may be staged. Stage NX indicatesthat the lymph nodes cannot be assessed (e.g., previously removed).Stage N0 indicates no regional lymph node metastasis. Stage N1 indicatesmetastasis to movable ipsilateral axillary lymph nodes. Stage N2indicates metastasis to ipsilateral axillary lymph nodes fixed to oneanother or to other structures. Stage N3 indicates metastasis toipsilateral internal mammary lymph nodes. Id.

Stage determination has potential prognostic value and provides criteriafor designing optimal therapy. Simpson et al., J. Clin. Oncology 18:2059(2000). Generally, pathological staging of breast cancer is preferableto clinical staging because the former gives a more accurate prognosis.However, clinical staging would be preferred if it were as accurate aspathological staging because it does not depend on an invasive procedureto obtain tissue for pathological evaluation. Staging of breast cancerwould be improved by detecting new markers in cells, tissues, or bodilyfluids which could differentiate between different stages of invasion.Progress in this field will allow more rapid and reliable method fortreating breast cancer patients.

Treatment of breast cancer is generally decided after an accuratestaging of the primary tumor. Primary treatment options include breastconserving therapy (lumpectomy, breast irradiation, and surgical stagingof the axilla), and modified radical mastectomy. Additional treatmentsinclude chemotherapy, regional irradiation, and, in extreme cases,terminating estrogen production by ovarian ablation.

Until recently, the customary treatment for all breast cancer wasmastectomy. Fonseca et al., Annals of Internal Medicine 127:1013 (1997).However, recent data indicate that less radical procedures may beequally effective, in terms of survival, for early stage breast cancer.Fisher et al., J. of Clinical Oncology 16:441 (1998). The treatmentoptions for a patient with early stage breast cancer (i.e., stage Tis)may be breast-sparing surgery followed by localized radiation therapy atthe breast. Alternatively, mastectomy optionally coupled with radiationor breast reconstruction may be employed. These treatment methods areequally effective in the early stages of breast cancer.

Patients with stage I and stage II breast cancer require surgery withchemotherapy and/or hormonal therapy. Surgery is of limited use in stageIII and stage IV patients. Thus, these patients are better candidatesfor chemotherapy and radiation therapy with surgery limited to biopsy topermit initial staging or subsequent restaging because cancer is rarelycurative at this stage of the disease. AJCC Cancer Staging Handbook 84,164-65 (Irvin D. Fleming et al. eds., 5^(th) ed. 1998).

In an effort to provide more treatment options to patients, efforts areunderway to define an earlier stage of breast cancer with low recurrencewhich could be treated with lumpectomy without postoperative radiationtreatment. While a number of attempts have been made to classify earlystage breast cancer, no consensus recommendation on postoperativeradiation treatment has been obtained from these studies. Page et al.,Cancer 75:1219 (1995); Fisher et al., Cancer 75:1223 (1995); Silversteinet al., Cancer 77:2267 (1996).

As discussed above, each of the methods for diagnosing and stagingovarian, and breast cancer is limited by the technology employed.Accordingly, there is need for sensitive molecular and cellular markersfor the detection of ovarian, and breast cancer as well as pancreaticcancer. There is a need for molecular markers for the accurate staging,including clinical and pathological staging, of ovarian, pancreatic orbreast cancers to optimize treatment methods. Finally, there is a needfor sensitive molecular and cellular markers to monitor the progress ofcancer treatments, including markers that can detect recurrence ofovarian, pancreatic or breast cancers following remission.

The present invention provides alternative methods of treating ovarian,pancreatic or breast cancer that overcome the limitations ofconventional therapeutic methods as well as offer additional advantagesthat will be apparent from the detailed description below.

Growth and metastasis of solid tumors are also dependent onangiogenesis. Folkman, J., 1986, Cancer Research, 46, 467-473; Folkman,J., 1989, Journal of the National Cancer Institute, 82, 4-6. It has beenshown, for example, that tumors which enlarge to greater than 2 mm mustobtain their own blood supply and do so by inducing the growth of newcapillary blood vessels. Once these new blood vessels become embedded inthe tumor, they provide a means for tumor cells to enter the circulationand metastasize to distant sites such as liver, lung or bone. Weidner,N., et al., 1991, The New England Journal of Medicine, 324(1), 1-8.

Angiogenesis, defined as the growth or sprouting of new blood vesselsfrom existing vessels, is a complex process that primarily occurs duringembryonic development The process is distinct from vasculogenesis, inthat the new endothelial cells lining the vessel arise fromproliferation of existing cells, rather than differentiating from stemcells. The process is invasive and dependent upon proteolysis of theextracellular matrix (ECM), migration of new endothelial cells, andsynthesis of new matrix components. Angiogenesis occurs duringembryogenic development of the circulatory system; however, in adulthumans, angiogenesis only occurs as a response to a pathologicalcondition (except during the reproductive cycle in women).

Under normal physiological conditions in adults, angiogenesis takesplace only in very restricted situations such as hair growth andwounding healing. Auerbach, W. and Auerbach, R., 1994, Pharmacol Ther.63(3):265-3 11; Ribatti et al., 1991, Haematologica 76(4):3 11-20;Risau, 1997, Nature 386(6626):67 1-4. Angiogenesis progresses by astimulus which results in the formation of a migrating column ofendothelial cells. Proteolytic activity is focused at the advancing tipof this “vascular sprout”, which breaks down the ECM sufficiently topermit the column of cells to infiltrate and migrate. Behind theadvancing front, the endothelial cells differentiate and begin to adhereto each other, thus forming a new basement membrane. The cells thencease proliferation and finally define a lumen for the new arteriole orcapillary.

Unregulated angiogenesis has gradually been recognized to be responsiblefor a wide range of disorders, including, but not limited to, cancer,cardiovascular disease, rheumatoid arthritis, psoriasis and diabeticretinopathy. Folkman, 1995, Nat Med 1(1):27-31; Isner, 1999, Circulation99(13): 1653-5; Koch, 1998, Arthritis Rheum 41(6):951-62; Walsh, 1999,Rheumatology (Oxford) 38(2):103-12; Ware and Simons, 1997, Nat Med 3(2):158-64.

Of particular interest is the observation that angiogenesis is requiredby solid tumors for their growth and metastases. Folkman, 1986 supra;Folkman 1990, J Natl. Cancer Inst., 82(1) 4-6; Folkman, 1992, SeminCancer Biol 3(2):65-71; Zetter, 1998, Annu Rev Med 49:407-24. A tumorusually begins as a single aberrant cell which can proliferate only to asize of a few cubic millimeters due to the distance from availablecapillary beds, and it can stay ‘dormant’ without further growth anddissemination for a long period of time. Some tumor cells then switch tothe angiogenic phenotype to activate endothelial cells, whichproliferate and mature into new capillary blood vessels. These newlyformed blood vessels not only allow for continued growth of the primarytumor, but also for the dissemination and recolonization of metastatictumor cells. The precise mechanisms that control the angiogenic switchis not well understood, but it is believed that neovascularization oftumor mass results from the net balance of a multitude of angiogenesisstimulators and inhibitors Folkman, 1995, supra.

One of the most potent angiogenesis inhibitors is endostatin identifiedby O'Reilly and Folkman. O'Reilly et al., 1997, Cell 88(2):277-85;O'Reilly et al., 1994, Cell 79(2):3 15-28. Its discovery was based onthe phenomenon that certain primary tumors can inhibit the growth ofdistant metastases. O'Reilly and Folkman hypothesized that a primarytumor initiates angiogenesis by generating angiogenic stimulators inexcess of inhibitors. However, angiogenic inhibitors, by virtue of theirlonger half life in the circulation, reach the site of a secondary tumorin excess of the stimulators. The net result is the growth of primarytumor and inhibition of secondary tumor. Endostatin is one of a growinglist of such angiogenesis inhibitors produced by primary tumors. It is aproteolytic fragment of a larger protein: endostatin is a 20 kDafragment of collagen XVIII (amino acid H1132-K1315 in murine collagenXVIII). Endostatin has been shown to specifically inhibit endothelialcell proliferation in vitro and block angiogenesis in vivo. Moreimportantly, administration of endostatin to tumor-bearing mice leads tosignificant tumor regression, and no toxicity or drug resistance hasbeen observed even after multiple treatment cycles. Boehm et al., 1997,Nature 390(6658):404-407. The fact that endostatin targets geneticallystable endothelial cells and inhibits a variety of solid tumors makes ita very attractive candidate for anticancer therapy. Fidler and Ellis,1994, Cell 79(2):185-8; Gastl et al., 1997, Oncology 54(3):177-84;Hinsbergh et al., 1999, Ann Oncol 10 Suppl 4:60-3. In addition,angiogenesis inhibitors have been shown to be more effective whencombined with radiation and chemotherapeutic agents. Klement, 2000, J.Clin Invest, 105(8) R15-24. Browder, 2000, Cancer Res. 6-(7) 1878-86,Arap et al., 1998, Science 279(5349):377-80; Mauceri et al., 1998,Nature 394(6690):287-91.

SUMMARY OF THE INVENTION

The present invention solves many needs in the art by providing nucleicacid molecules, polypeptides and antibodies thereto, variants andderivatives of the nucleic acids and polypeptides, and agonists andantagonists thereto that may be used to identify, diagnose, monitor,stage, image and treat ovarian cancer and/or non-cancerous diseasestates in ovarian; identify and monitor ovarian tissue; and identify anddesign agonists and antagonists of polypeptides of the invention. Theinvention also provides gene therapy, methods for producing transgenicanimals and cells, and methods for producing engineered ovarian tissuefor treatment and research.

One aspect of the present invention relates to nucleic acid moleculesthat are specific to ovarian cells, ovarian tissue and/or the ovarianorgan. These ovarian specific nucleic acids (OSNAs) may be a naturallyoccurring cDNA, genomic DNA, RNA, or a fragment of one of these nucleicacids, or may be a non-naturally occurring nucleic acid molecule. If theOSNA is genomic DNA, then the OSNA is an ovarian specific gene (OSG). Ifthe OSNA is RNA, then it is an ovarian specific transcript encoded by anOSG. Due to alternative splicing and transcriptional modification oneOSG may encode for multiple ovarian specific RNAs. In a preferredembodiment, the nucleic acid molecule encodes a polypeptide that isspecific to ovarian. More preferred is a nucleic acid molecule thatencodes a polypeptide comprising an amino acid sequence of SEQ ID NO:129-295. In another preferred embodiment, the nucleic acid moleculecomprises a nucleic acid sequence of SEQ ID NO: 1-128. For the OSNAsequences listed herein, DEX0455_(—)001.nt.1 corresponds to SEQ IDNO: 1. For sequences with multiple splice variants, the parent sequenceDEX0455_(—)001.nt.1, will be followed by DEX0455_(—)001.nt.2, etc. foreach splice variant. The sequences off the corresponding peptides arelisted as DEX0455_(—)001.aa.1, etc. For the mapping of all of thenucleotides and peptides, see the table in the Example 1 section below.

This aspect of the present invention also relates to nucleic acidmolecules that selectively hybridize or exhibit substantial sequencesimilarity to nucleic acid molecules encoding an Ovarian SpecificProtein (OSP), or that selectively hybridize or exhibit substantialsequence similarity to an OSNA. In one embodiment of the presentinvention the nucleic acid molecule comprises an allelic variant of anucleic acid molecule encoding an OSP, or an allelic variant of an OSNA.In another embodiment, the nucleic acid molecule comprises a part of anucleic acid sequence that encodes an OSP or a part of a nucleic acidsequence of an OSNA.

In addition, this aspect of the present invention relates to a nucleicacid molecule further comprising one or more expression controlsequences controlling the transcription and/or translation of all or apart of an OSNA or the transcription and/or translation of a nucleicacid molecule that encodes all or a fragment of an OSP.

Another aspect of the present invention relates to vectors and/or hostcells comprising a nucleic acid molecule of this invention. In apreferred embodiment, the nucleic acid molecule of the vector and/orhost cell encodes all or a fragment of an OSP. In another preferredembodiment, the nucleic acid molecule of the vector and/or host cellcomprises all or a part of an OSNA. Vectors and host cells of thepresent invention are useful in the recombinant production ofpolypeptides, particularly OSPs of the present invention.

Another aspect of the present invention relates to polypeptides encodedby a nucleic acid molecule of this invention. The polypeptide maycomprise either a fragment or a full-length protein. In a preferredembodiment, the polypeptide is an OSP. However, this aspect of thepresent invention also relates to mutant proteins (muteins) of OSPs,fusion proteins of which a portion is an OSP, and proteins andpolypeptides encoded by allelic variants of an OSNA as provided herein.

A further aspect of the present invention is a novel splice variantwhich encodes an amino acid sequence that provides a novel region to betargeted for the generation of reagents that can be used in thedetection and/or treatment of cancer. The novel amino acid sequence maylead to a unique protein structure, protein subcellular localization,biochemical processing or function. This information can be used todirectly or indirectly facilitate the generation of additional or noveltherapeutics or diagnostics. The nucleotide sequence in this novelsplice variant can be used as a nucleic acid probe for the diagnosisand/or treatment of cancer.

Another aspect of the present invention relates to antibodies and otherbinders that specifically bind to a polypeptide of the instantinvention. Accordingly antibodies or binders of the present inventionspecifically bind to OSPs, muteins, fusion proteins, and/or homologousproteins or polypeptides encoded by allelic variants of an OSNA asprovided herein.

Another aspect of the present invention relates to agonists andantagonists of the nucleic acid molecules and polypeptides of thisinvention. The agonists and antagonists of the instant invention may beused to treat ovarian cancer and non-cancerous disease states in ovarianand to produce engineered ovarian tissue.

Another aspect of the present invention relates to methods for using thenucleic acid molecules to detect or amplify nucleic acid molecules thathave similar or identical nucleic acid sequences compared to the nucleicacid molecules described herein. Such methods are useful in identifying,diagnosing, monitoring, staging, imaging and treating ovarian cancerand/or non-cancerous disease states in ovarian. Such methods are alsouseful in identifying and/or monitoring ovarian tissue. In addition,measurement of levels of one or more of the nucleic acid molecules ofthis invention may be useful as a diagnostic as part of a panel incombination with known other markers, particularly those described inthe ovarian cancer background section above.

Another aspect of the present invention relates to use of the nucleicacid molecules of this invention in gene therapy, for producingtransgenic animals and cells, and for producing engineered ovariantissue for treatment and research.

Another aspect of the present invention relates to methods for detectingpolypeptides of this invention, preferably using antibodies thereto.Such methods are useful to identify, diagnose, monitor, stage, image andtreat ovarian cancer and non-cancerous disease states in ovarian. Inaddition, measurement of levels of one or more of the polypeptides ofthis invention may be useful to identify, diagnose, monitor, stage,and/or image ovarian cancer in combination with known other markers,particularly those described in the ovarian cancer background sectionabove. The polypeptides of the present invention can also be used toidentify and/or monitor ovarian tissue, and to produce engineeredovarian tissue.

Yet another aspect of the present invention relates to a computerreadable means of storing the nucleic acid and amino acid sequences ofthe invention. The records of the computer readable means can beaccessed for reading and displaying of sequences for comparison,alignment and ordering of the sequences of the invention to othersequences. In addition, the computer records regarding the nucleic acidand/or amino acid sequences and/or measurements of their levels may beused alone or in combination with other markers to diagnose ovarianrelated diseases.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.nt.5 (SEQ ID NO:96;EpCAM) and DEX0455_(—)049.nt.1 (SEQ ID NO:92; Ovr232);

FIG. 2 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.aa.5 (SEQ ID NO:255;EpCAM) and DEX0455_(—)049.aa.1 (SEQ ID NO:251; Ovr232);

FIG. 3 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.nt.5 (SEQ ID NO:96;EpCAM) and DEX0455_(—)049.nt.2 (SEQ ID NO:93; Ovr232v1);

FIG. 4 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.aa.5 (SEQ ID NO:255;EpCAM) and DEX0455_(—)049.aa.2 (SEQ ID NO:252; Ovr232v1);

FIG. 5 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.nt.5 (SEQ ID NO:96;EpCAM) and DEX0455_(—)049.nt.3 (SEQ ID NO:94; Ovr232v2);

FIG. 6 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.aa.5 (SEQ ID NO:255;EpCAM) and DEX0455_(—)049.aa.3 (SEQ ID NO:253; Ovr232v2);

FIG. 7 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.nt.5 (SEQ ID NO:96;EpCAM) and DEX0455_(—)049.nt.4 (SEQ ID NO:95; Ovr232v3);

FIG. 8 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)049.aa.5 (SEQ ID NO:255;EpCAM) and DEX0455_(—)049.aa.4 (SEQ ID NO:254; Ovr232v3);

FIG. 9 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.nt.1 (SEQ ID NO:98;Ovr107) and DEX0455_(—)051.nt.2 (SEQ ID NO:99);

FIG. 10 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.aa.1 (SEQ ID NO:258;Ovr107) and DEX0455_(—)051.aa.3 (SEQ ID NO:260);

FIG. 11 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.aa.1 (SEQ ID NO:258;Ovr107) and DEX0455_(—)051.aa.2 (SEQ ID NO:259);

FIG. 12 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.nt.1 (SEQ ID NO:98;Ovr107) and DEX0455_(—)051.nt.3 (SEQ ID NO:100);

FIG. 13 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.nt.1 (SEQ ID NO:98;Ovr107) and DEX0455_(—)051.nt.4 (SEQ ID NO: 101);

FIG. 14 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.nt.1 (SEQ ID NO:98;Ovr107) and DEX0455_(—)051.nt.5 (SEQ ID NO: 102);

FIG. 15 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)051.nt.1 (SEQ ID NO:98;Ovr107) and DEX0455_(—)051.nt.6 (SEQ ID NO: 103; Ovr107v4);

FIG. 16 is a nucleotide sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)053.nt.1 (SEQ ID NO: 108;Ovr110) and DEX0455_(—)053.nt.2 (SEQ ID NO: 109; Ovr110v1);

FIG. 17 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)053.aa.1 (SEQ ID NO:268;Ovr110) and DEX0455_(—)053.aa.2 (SEQ ID NO:269);

FIG. 18 is an amino acid sequence alignment which shows regions ofsimilarity and difference between DEX0455_(—)053.aa.1 (SEQ ID NO:268;Ovr110) and DEX0455_(—)053.aa.3 (SEQ ID NO:270).

DETAILED DESCRIPTION OF THE INVENTION

Definitions and General Techniques

Unless otherwise defined herein, scientific and technical terms used inconnection with the present invention shall have the meanings that arecommonly understood by those of ordinary skill in the art. Further,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. Generally,nomenclatures used in connection with, and techniques of, cell andtissue culture, molecular biology, immunology, microbiology, geneticsand protein and nucleic acid chemistry and hybridization describedherein are those well known and commonly used in the art. The methodsand techniques of the present invention are generally performedaccording to conventional methods well known in the art and as describedin various general and more specific references that are cited anddiscussed throughout the present specification unless otherwiseindicated. See, e.g., Sambrook et al., Molecular Cloning: A LaboratoryManual, 2d ed., Cold Spring Harbor Laboratory Press (1989) and Sambrooket al., Molecular Cloning: A Laboratory Manual, 3d ed., Cold SpringHarbor Press (2001); Ausubel et al., Current Protocols in MolecularBiology, Greene Publishing Associates (1992, and Supplements to 2000);Ausubel et al., Short Protocols in Molecular Biology: A Compendium ofMethods from Current Protocols in Molecular Biology—4th Ed., Wiley &Sons (1999); Harlow and Lane, Antibodies: A Laboratory Manual, ColdSpring Harbor Laboratory Press (1990); and Harlow and Lane, UsingAntibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press(1999).

Enzymatic reactions and purification techniques are performed accordingto manufacturer's specifications, as commonly accomplished in the art oras described herein. The nomenclatures used in connection with, and thelaboratory procedures and techniques of, analytical chemistry, syntheticorganic chemistry, and medicinal and pharmaceutical chemistry describedherein are those well known and commonly used in the art. Standardtechniques are used for chemical syntheses, chemical analyses,pharmaceutical preparation, formulation, and delivery, and treatment ofpatients.

The following terms, unless otherwise indicated, shall be understood tohave the following meanings:

A “nucleic acid molecule” of this invention refers to a polymeric formof nucleotides and includes both sense and antisense strands of RNA,cDNA, genomic DNA, and synthetic forms and mixed polymers of the above.A nucleotide refers to a ribonucleotide, deoxynucleotide or a modifiedform of either type of nucleotide. A “nucleic acid molecule” as usedherein is synonymous with “nucleic acid” and “polynucleotide.” The term“nucleic acid molecule” usually refers to a molecule of at least 10bases in length, unless otherwise specified. The term includes single-and double-stranded forms of DNA. In addition, a polynucleotide mayinclude either or both naturally occurring and modified nucleotideslinked together by naturally occurring and/or non-naturally occurringnucleotide linkages.

Nucleotides are represented by single letter symbols in nucleic acidmolecule sequences. The following table lists symbols identifyingnucleotides or groups of nucleotides which may occupy the symbolposition on a nucleic acid molecule. See Nomenclature Committee of theInternational Union of Biochemistry (NC-IUB), Nomenclature forincompletely specified bases in nucleic acid sequences, Recommendations1984., Eur J Biochem. 150(1):1-5 (1985). Complementary Symbol MeaningGroup/Origin of Designation Symbol a a Adenine t/u g g Guanine c c cCytosine g t t Thymine a u u Uracil a r g or a puRine y y t/u or cpYrimidine r m a or c aMino k k g or t/u Keto m s g or c Stronginteractions 3H-bonds w w a or t/u Weak interactions 2H-bonds s b g or cor t/u not a v d a or g or t/u not c h h a or c or t/u not g d v a or gor c not t, not u b n a or g or c aNy n or t/u, unknown, or other

The nucleic acid molecules may be modified chemically or biochemicallyor may contain non-natural or derivatized nucleotide bases, as will bereadily appreciated by those of skill in the art. Such modificationsinclude, for example, labels, methylation, substitution of one or moreof the naturally occurring nucleotides with an analog, internucleotidemodifications such as uncharged linkages (e.g., methyl phosphonates,phosphotriesters, phosphoramidates, carbamates, etc.), charged linkages(e.g., phosphorothioates, phosphorodithioates, etc.), pendent moieties(e.g., polypeptides), intercalators (e.g., acridine, psoralen, etc.),chelators, alkylators, and modified linkages (e.g., alpha anomericnucleic acids, etc.) The term “nucleic acid molecule” also includes anytopological conformation, including single-stranded, double-stranded,partially duplexed, triplexed, hairpinned, circular and padlockedconformations. Also included are synthetic molecules that mimicpolynucleotides in their ability to bind to a designated sequence viahydrogen bonding and other chemical interactions. Such molecules areknown in the art and include, for example, those in which peptidelinkages substitute for phosphate linkages in the backbone of themolecule.

A “gene” is defined as a nucleic acid molecule that comprises a nucleicacid sequence that encodes a polypeptide and the expression controlsequences that surround the nucleic acid sequence that encodes thepolypeptide. For instance, a gene may comprise a promoter, one or moreenhancers, a nucleic acid sequence that encodes a polypeptide,downstream regulatory sequences and, possibly, other nucleic acidsequences involved in regulation of the expression of an RNA. As is wellknown in the art, eukaryotic genes usually contain both exons andintrons. The term “exon” refers to a nucleic acid sequence found ingenomic DNA that is bioinformatically predicted and/or experimentallyconfirmed to contribute contiguous sequence to a mature mRNA transcript.The term “intron” refers to a nucleic acid sequence found in genomic DNAthat is predicted and/or confirmed to not contribute to a mature mRNAtranscript, but rather to be “spliced out” during processing of thetranscript.

A nucleic acid molecule or polypeptide is “derived” from a particularspecies if the nucleic acid molecule or polypeptide has been isolatedfrom the particular species, or if the nucleic acid molecule orpolypeptide is homologous to a nucleic acid molecule or polypeptideisolated from a particular species.

An “isolated” or “substantially pure” nucleic acid or polynucleotide(e.g., an RNA, DNA or a mixed polymer) is one which is substantiallyseparated from other cellular components that naturally accompany thenative polynucleotide in its natural host cell, e.g., ribosomes,polymerases, or genomic sequences with which it is naturally associated.The term embraces a nucleic acid or polynucleotide that (1) has beenremoved from its naturally occurring environment, (2) is not associatedwith all or a portion of a polynucleotide in which the “isolatedpolynucleotide” is found in nature, (3) is operatively linked to apolynucleotide which it is not linked to in nature, (4) does not occurin nature as part of a larger sequence or (5) includes nucleotides orinternucleoside bonds that are not found in nature. The term “isolated”or “substantially pure” also can be used in reference to recombinant orcloned DNA isolates, chemically synthesized polynucleotide analogs, orpolynucleotide analogs that are biologically synthesized by heterologoussystems. The term “isolated nucleic acid molecule” includes nucleic acidmolecules that are integrated into a host cell chromosome at aheterologous site, recombinant fusions of a native fragment to aheterologous sequence, recombinant vectors present as episomes or asintegrated into a host cell chromosome.

A “part” of a nucleic acid molecule refers to a nucleic acid moleculethat comprises a partial contiguous sequence of at least 10 bases of thereference nucleic acid molecule. Preferably, a part comprises at least15 to 20 bases of a reference nucleic acid molecule. In theory, anucleic acid sequence of 17 nucleotides is of sufficient length to occurat random less frequently than once in the three gigabase human genome,and thus provides a nucleic acid probe that can uniquely identify thereference sequence in a nucleic acid mixture of genomic complexity. Apreferred part is one that comprises a nucleic acid sequence that canencode at least 6 contiguous amino acid sequences (fragments of at least18 nucleotides) because they are useful in directing the expression orsynthesis of peptides that are useful in mapping the epitopes of thepolypeptide encoded by the reference nucleic acid. See, e.g., Geysen etal., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1984); and U.S. Pat. Nos.4,708,871 and 5,595,915, the disclosures of which are incorporatedherein by reference in their entireties. A part may also comprise atleast 25, 30, 35 or 40 nucleotides of a reference nucleic acid molecule,or at least 50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400 or 500nucleotides of a reference nucleic acid molecule. A part of a nucleicacid molecule may comprise no other nucleic acid sequences.Alternatively, a part of a nucleic acid may comprise other nucleic acidsequences from other nucleic acid molecules.

The term “oligonucleotide” refers to a nucleic acid molecule generallycomprising a length of 200 bases or fewer. The term often refers tosingle-stranded deoxyribonucleotides, but it can refer as well tosingle-or double-stranded ribonucleotides, RNA:DNA hybrids anddouble-stranded DNAs, among others. Preferably, oligonucleotides are 10to 60 bases in length and most preferably 12, 13, 14, 15, 16, 17, 18, 19or 20 bases in length. Other preferred oligonucleotides are 25, 30, 35,40, 45, 50, 55 or 60 bases in length. Oligonucleotides may besingle-stranded, e.g. for use as probes or primers, or may bedouble-stranded, e.g. for use in the construction of a mutant gene.Oligonucleotides of the invention can be either sense or antisenseoligonucleotides. An oligonucleotide can be derivatized or modified asdiscussed above for nucleic acid molecules.

Oligonucleotides, such as single-stranded DNA probe oligonucleotides,often are synthesized by chemical methods, such as those implemented onautomated oligonucleotide synthesizers. However, oligonucleotides can bemade by a variety of other methods, including in vitro recombinantDNA-mediated techniques and by expression of DNAs in cells andorganisms. Initially, chemically synthesized DNAs typically are obtainedwithout a 5′ phosphate. The 5′ ends of such oligonucleotides are notsubstrates for phosphodiester bond formation by ligation reactions thatemploy DNA ligases typically used to form recombinant DNA molecules.Where ligation of such oligonucleotides is desired, a phosphate can beadded by standard techniques, such as those that employ a kinase andATP. The 3′ end of a chemically synthesized oligonucleotide generallyhas a free hydroxyl group and, in the presence of a ligase, such as T4DNA ligase, readily will form a phosphodiester bond with a 5′ phosphateof another polynucleotide, such as another oligonucleotide. As is wellknown, this reaction can be prevented selectively, where desired, byremoving the 5′ phosphates of the other polynucleotide(s) prior toligation.

The term “naturally occurring nucleotide” referred to herein includesnaturally occurring deoxyribonucleotides and ribonucleotides. The term“modified nucleotides” referred to herein includes nucleotides withmodified or substituted sugar groups and the like. The term “nucleotidelinkages” referred to herein includes nucleotide linkages such asphosphorothioate, phosphorodithioate, phosphoroselenoate,phosphorodiselenoate, phosphoroanilothioate, phoshoraniladate,phosphoroamidate, and the like. See e.g., LaPlanche et al. Nucl. AcidsRes. 14:9081-9093 (1986); Stein et al. Nucl. Acids Res. 16:3209-3221(1988); Zon et al. Anti-Cancer Drug Design 6:539-568 (1991); Zon et al.,in Eckstein (ed.) Oligonucleotides and Analogues: A Practical Approach,pp. 87-108, Oxford University Press (1991); Uhlmann and Peyman ChemicalReviews 90:543 (1990), and U.S. Pat. No. 5,151,510, the disclosure ofwhich is hereby incorporated by reference in its entirety.

Unless specified otherwise, the left hand end of a polynucleotidesequence in sense orientation is the 5′ end and the right hand end ofthe sequence is the 3′ end. In addition, the left hand direction of apolynucleotide sequence in sense orientation is referred to as the 5′direction, while the right hand direction of the polynucleotide sequenceis referred to as the 3′ direction. Further, unless otherwise indicated,each nucleotide sequence is set forth herein as a sequence ofdeoxyribonucleotides. It is intended, however, that the given sequencebe interpreted as would be appropriate to the polynucleotidecomposition: for example, if the isolated nucleic acid is composed ofRNA, the given sequence intends ribonucleotides, with uridinesubstituted for thymidine.

The term “allelic variant” refers to one of two or more alternativenaturally occurring forms of a gene, wherein each gene possesses aunique nucleotide sequence. In a preferred embodiment, different allelesof a given gene have similar or identical biological properties.

The term “percent sequence identity” in the context of nucleic acidsequences refers to the residues in two sequences which are the samewhen aligned for maximum correspondence. The length of sequence identitycomparison may be over a stretch of at least about nine nucleotides,usually at least about 20 nucleotides, more usually at least about 24nucleotides, typically at least about 28 nucleotides, more typically atleast about 32 nucleotides, and preferably at least about 36 or morenucleotides. There are a number of different algorithms known in the artwhich can be used to measure nucleotide sequence identity. For instance,polynucleotide sequences can be compared using FASTA, Gap or Bestfit,which are programs in Wisconsin Package Version 10.0, Genetics ComputerGroup (GCG), Madison, Wisc. FASTA, which includes, e.g., the programsFASTA2 and FASTA3, provides alignments and percent sequence identity ofthe regions of the best overlap between the query and search sequences(Pearson, Methods Enzymol. 183: 63-98 (1990); Pearson, Methods Mol.Biol. 132: 185-219 (2000); Pearson, Methods Enzymol. 266: 227-258(1996); Pearson, J. Mol. Biol. 276: 71-84 (1998)). Unless otherwisespecified, default parameters for a particular program or algorithm areused. For instance, percent sequence identity between nucleic acidsequences can be determined using FASTA with its default parameters (aword size of 6 and the NOPAM factor for the scoring matrix) or using Gapwith its default parameters as provided in GCG Version 6.1.

A reference to a nucleic acid'sequence encompasses its complement unlessotherwise specified. Thus, a reference to a nucleic acid molecule havinga particular sequence should be understood to encompass itscomplementary strand, with its complementary sequence. The complementarystrand is also useful, e.g., for antisense therapy, double-stranded RNA(dsRNA) inhibition (RNAi), combination of triplex and antisense,hybridization probes and PCR primers.

In the molecular biology art, researchers use the terms “percentsequence identity”, “percent sequence similarity” and “percent sequencehomology” interchangeably. In this application, these terms shall havethe same meaning with respect to nucleic acid sequences only.

The term “substantial similarity” or “substantial sequence similarity,”when referring to a nucleic acid or fragment thereof, indicates that,when optimally aligned with appropriate nucleotide insertions ordeletions with another nucleic acid (or its complementary strand), thereis nucleotide sequence identity in at least about 50%, more preferably60% of the nucleotide bases, usually at least about 70%, more usually atleast about 80%, preferably at least about 90%, and more preferably atleast about 95-98% of the nucleotide bases, as measured by any wellknown algorithm of sequence identity, such as FASTA, BLAST or Gap, asdiscussed above.

Alternatively, substantial similarity exists between a first and secondnucleic acid sequence when the first nucleic acid sequence or fragmentthereof hybridizes to an antisense strand of the second nucleic acid,under selective hybridization conditions. Typically, selectivehybridization will occur between the first nucleic acid sequence and anantisense strand of the second nucleic acid sequence when there is atleast about 55% sequence identity between the first and second nucleicacid sequences—preferably at least about 65%, more preferably at leastabout 75%, and most preferably at least about 90%—over a stretch of atleast about 14 nucleotides, more preferably at least 17 nucleotides,even more preferably at least 20, 25, 30, 35, 40, 50, 60, 70, 80, 90 or100 nucleotides.

Nucleic acid hybridization will be affected by such conditions as saltconcentration, temperature, solvents, the base composition of thehybridizing species, length of the complementary regions, and the numberof nucleotide base mismatches between the hybridizing nucleic acids, aswill be readily appreciated by those skilled in the art. “Stringenthybridization conditions” and “stringent wash conditions” in the contextof nucleic acid hybridization experiments depend upon a number ofdifferent physical parameters. The most important parameters includetemperature of hybridization, base composition of the nucleic acids,salt concentration and length of the nucleic acid. One having ordinaryskill in the art knows how to vary these parameters to achieve aparticular stringency of hybridization. In general, “stringenthybridization” is performed at about 25° C. below the thermal meltingpoint (T_(m)) for the specific DNA hybrid under a particular set ofconditions. “Stringent washing” is performed at temperatures about 5° C.lower than the T_(m) for the specific DNA hybrid under a particular setof conditions. The T_(m) is the temperature at which 50% of the targetsequence hybridizes to a perfectly matched probe. See Sambrook (1989),supra, p. 9.51.

The T_(m) for a particular DNA-DNA hybrid can be estimated by theformula:T _(m)=81.5° C.+16.6(log₁₀[Na⁺])+0.41(fraction G+C)−0.63(%formamide)−(600/l) where l is the length of the hybrid in base pairs.

The T_(m) for a particular RNA-RNA hybrid can be estimated by theformula:T _(m)=79.8° C.+18.5(log₁₀[Na⁺])+0.58(fraction G+C)+11.8(fractionG+C)²−0.35(% formamide)−(820/l).

The T_(m) for a particular RNA-DNA hybrid can be estimated by theformula:T _(m)=79.8° C.+18.5(log₁₀[Na⁺])+0.58(fraction G+C)+11.8(fractionG+C)²−0.50(% formamide)−(820/l).

In general, the T_(m) decreases by 1-1.5° C. for each 1% of mismatchbetween two nucleic acid sequences. Thus, one having ordinary skill inthe art can alter hybridization and/or washing conditions to obtainsequences that have higher or lower degrees of sequence identity to thetarget nucleic acid. For instance, to obtain hybridizing nucleic acidsthat contain up to 10% mismatch from the target nucleic acid sequence,10-15° C. would be subtracted from the calculated T_(m) of a perfectlymatched hybrid, and then the hybridization and washing temperaturesadjusted accordingly. Probe sequences may also hybridize specifically toduplex DNA under certain conditions to form triplex or other higherorder DNA complexes. The preparation of such probes and suitablehybridization conditions are well known in the art.

An example of stringent hybridization conditions for hybridization ofcomplementary nucleic acid sequences having more than 100 complementaryresidues on a filter in a Southern or Northern blot or for screening alibrary is 50% formamide/6×SSC at 42° C. for at least ten hours andpreferably overnight (approximately 16 hours). Another example ofstringent hybridization conditions is 6×SSC at 68° C. without formamidefor at least ten hours and preferably overnight An example of moderatestringency hybridization conditions is 6×SSC at 55° C. without formamidefor at least ten hours and preferably overnight. An example of lowstringency hybridization conditions for hybridization of complementarynucleic acid sequences having more than 100 complementary residues on afilter in a Southern or northern blot or for screening a library is6×SSC at 42° C. for at least ten hours. Hybridization conditions toidentify nucleic acid sequences that are similar but not identical canbe identified by experimentally changing the hybridization temperaturefrom 68° C. to 42° C. while keeping the salt concentration constant(6×SSC), or keeping the hybridization temperature and salt concentrationconstant (e.g. 42° C. and 6×SSC) and varying the formamide concentrationfrom 50% to 0%. Hybridization buffers may also include blocking agentsto lower background. These agents are well known in the art. SeeSambrook et al. (1989), supra, pages 8.46 and 9.46-9.58. See alsoAusubel (1992), supra, Ausubel (1999), supra, and Sambrook (2001),supra.

Wash conditions also can be altered to change stringency conditions. Anexample of stringent wash conditions is a 0.2×SSC wash at 65° C. for 15minutes (see Sambrook (1989), supra, for SSC buffer). Often the highstringency wash is preceded by a low stringency wash to remove excessprobe. An exemplary medium stringency wash for duplex DNA of more than100 base pairs is 1×SSC at 45° C. for 15 minutes. An exemplary lowstringency wash for such a duplex is 4×SSC at 40° C. for 15 minutes. Ingeneral, signal-to-noise ratio of 2× or higher than that observed for anunrelated probe in the particular hybridization assay indicatesdetection of a specific hybridization.

As defined herein, nucleic acids that do not hybridize to each otherunder stringent conditions are still substantially similar to oneanother if they encode polypeptides that are substantially identical toeach other. This occurs, for example, when a nucleic acid is createdsynthetically or recombinantly using a high codon degeneracy aspermitted by the redundancy of the genetic code.

Hybridization conditions for nucleic acid molecules that are shorterthan 100 nucleotides in length (e.g., for oligonucleotide probes) may becalculated by the formula:

T_(m)=81.5° C.+16.6(log₁₀[Na⁺])+0.41(fraction G+C)−(600/N), wherein N ischange length and the [Na⁺] is 1 M or less. See Sambrook (1989), supra,p. 11.46. For hybridization of probes shorter than 100 nucleotides,hybridization is usually performed under stringent conditions (5-10° C.below the T_(m)) using high concentrations (0.1-1.0 pmol/ml) of probe.Id. at p. 11.45. Determination of hybridization using mismatched probes,pools of degenerate probes or “guessmers,” as well as hybridizationsolutions and methods for empirically determining hybridizationconditions are well known in the art. See, e.g., Ausubel (1999), supra;Sambrook (1989), supra, pp. 11.45-11.57.

The term “digestion” or “digestion of DNA” refers to catalytic cleavageof the DNA with a restriction enzyme that acts only at certain sequencesin the DNA. The various restriction enzymes referred to herein arecommercially available and their reaction conditions, cofactors andother requirements for use are known and routine to the skilled artisan.For analytical purposes, typically, 1 μg of plasmid or DNA fragment isdigested with about 2 units of enzyme in about 20 μl of reaction buffer.For the purpose of isolating DNA fragments for plasmid construction,typically 5 to 50 μg of DNA are digested with 20 to 250 units of enzymein proportionately larger volumes. Appropriate buffers and substrateamounts for particular restriction enzymes are described in standardlaboratory manuals, such as those referenced below, and are specified bycommercial suppliers. Incubation times of about 1 hour at 37° C. areordinarily used, but conditions may vary in accordance with standardprocedures, the supplier's instructions and the particulars of thereaction. After digestion, reactions may be analyzed, and fragments maybe purified by electrophoresis through an agarose or polyacrylamide gel,using well known methods that are routine for those skilled in the art.

The term “ligation” refers to the process of forming phosphodiesterbonds between two or more polynucleotides, which most often aredouble-stranded DNAs. Techniques for ligation are well known to the artand protocols for ligation are described in standard laboratory manualsand references, such as, e.g., Sambrook (1989), supra.

Genome-derived “single exon probes,” are probes that comprise at leastpart of an exon (“reference exon”) and can hybridize detectably underhigh stringency conditions to transcript-derived nucleic acids thatinclude the reference exon but do not hybridize detectably under highstringency conditions to nucleic acids that lack the reference exon.Single exon probes typically further comprise, contiguous to a first endof the exon portion, a first intronic and/or intergenic sequence that isidentically contiguous to the exon in the genome, and may contain asecond intronic and/or intergenic sequence that is identicallycontiguous to the exon in the genome. The minimum length ofgenome-derived single exon probes is defined by the requirement that theexonic portion be of sufficient length to hybridize under highstringency conditions to transcript-derived nucleic acids, as discussedabove. The maximum length of genome-derived single exon probes isdefined by the requirement that the probes contain portions of no morethan one exon. The single exon probes may contain priming sequences notfound in contiguity with the rest of the probe sequence in the genome,which priming sequences are useful for PCR and other amplification-basedtechnologies. In another aspect, the invention is directed to singleexon probes based on the OSNAs disclosed herein.

In one embodiment, the term “microarray” refers to a “nucleic acidmicroarray” having a substrate-bound plurality of nucleic acids,hybridization to each of the plurality of bound nucleic acids beingseparately detectable. The substrate can be solid or porous, planar ornon-planar, unitary or distributed. Nucleic acid microarrays include allthe devices so called in Schena (ed.), DNA Microarrays: A PracticalApproach (Practical Approach Series), Oxford University Press (1999);Nature Genet. 21(1)(suppl.):1-60 (1999); Schena (ed.), MicroarrayBiochip: Tools and Technology, Eaton Publishing Company/BioTechniquesBooks Division (2000). Additionally, these nucleic acid microarraysinclude a substrate-bound plurality of nucleic acids in which theplurality of nucleic acids are disposed on a plurality of beads, ratherthan on a unitary planar substrate, as is described, inter alia, inBrenner et al., Proc. Natl. Acad. Sci. USA 97(4):1665-1670 (2000).Examples of nucleic acid microarrays may be found in U.S. Pat. Nos.6,391,623, 6,383,754, 6,383,749, 6,380,377, 6,379,897, 6,376,191,6,372,431, 6,351,712 6,344,316, 6,316,193, 6,312,906, 6,309,828,6,309,824, 6,306,643, 6,300,063, 6,287,850, 6,284,497, 6,284,465,6,280,954, 6,262,216, 6,251,601, 6,245,518, 6,263,287, 6,251,601,6,238,866, 6,228,575, 6,214,587, 6,203,989, 6,171,797, 6,103,474,6,083,726, 6,054,274, 6,040,138, 6,083,726, 6,004,755, 6,001,309,5,958,342, 5,952,180, 5,936,731, 5,843,655, 5,814,454, 5,837,196,5,436,327, 5,412,087, and 5,405,783, the disclosures of which areincorporated herein by reference in their entireties.

In an alternative embodiment, a “microarray” may also refer to a“peptide microarray” or “protein microarray” having a substrate-boundcollection or plurality of polypeptides, the binding to each of theplurality of bound polypeptides being separately detectable.Alternatively, the peptide microarray may have a plurality of binders,including but not limited to monoclonal antibodies, polyclonalantibodies, phage display binders, yeast 2 hybrid binders, and aptamers,which can specifically detect the binding of the polypeptides of thisinvention. The array may be based on autoantibody detection to thepolypeptides of this invention, see Robinson et al, Nature Medicine8(3):295-301 (2002). Examples of peptide arrays may be found in WO02/31463, WO 02/25288, WO 01/94946, WO 01/88162, WO 01/68671, WO01/57259, WO 00/61806, WO 00/54046, WO 00/47774, WO 99/40434, WO99/39210, and WO 97/42507 and U.S. Pat. Nos. 6,268,210, 5,766,960, and5,143,854, the disclosures of which are incorporated herein by referencein their entireties.

In addition, determination of the levels of the OSNA or OSP may be madein a multiplex manner using techniques described in WO 02/29109, WO02/24959, WO 01/83502, WO 01/73113, WO 01/59432, WO 01/57269, and WO99/67641, the disclosures of which are incorporated herein by referencein their entireties.

The term “mutant”, “mutated”, or “mutation” when applied to nucleic acidsequences means that nucleotides in a nucleic acid sequence may beinserted, deleted or changed compared to a reference nucleic acidsequence. A single alteration may be made at a locus (a point mutation)or multiple nucleotides may be inserted, deleted or changed at a singlelocus. In addition, one or more alterations may be made at any number ofloci within a nucleic acid sequence. In a preferred embodiment of thepresent invention, the nucleic acid sequence is the wild type nucleicacid sequence encoding an OSP or is an OSNA. The nucleic acid sequencemay be mutated by any method known in the art including thosemutagenesis techniques described infra.

The term “error-prone PCR” refers to a process for performing PCR underconditions where the copying fidelity of the DNA polymerase is low, suchthat a high rate of point mutations is obtained along the entire lengthof the PCR product. See, e.g., Leung et al., Technique 1: 11-15 (1989)and Caldwell et al., PCR Methods Applic. 2: 28-33 (1992).

The term “oligonucleotide-directed mutagenesis” refers to a processwhich enables the generation of site-specific mutations in any clonedDNA segment of interest. See, e.g., Reidhaar-Olson et al., Science 241:53-57 (1988).

The term “assembly PCR” refers to a process which involves the assemblyof a PCR product from a mixture of small DNA fragments. A large numberof different PCR reactions occur in parallel in the same vial, with theproducts of one reaction priming the products of another reaction.

The term “sexual PCR mutagenesis” or “DNA shuffling” refers to a methodof error-prone PCR coupled with forced homologous recombination betweenDNA molecules of different but highly related DNA sequence in vitro,caused by random fragmentation of the DNA molecule based on sequencesimilarity, followed by fixation of the crossover by primer extension inan error-prone PCR reaction. See, e.g. Stemmer, Proc. Natl. Acad. Sci.U.S.A. 91: 10747-10751 (1994). DNA shuffling can be carried out betweenseveral related genes (“Family shuffling”).

The term “in vivo mutagenesis” refers to a process of generating randommutations in any cloned DNA of interest which involves the propagationof the DNA in a strain of bacteria such as E. coli that carriesmutations in one or more of the DNA repair pathways. These “mutator”strains have a higher random mutation rate than that of a wild-typeparent Propagating the DNA in a mutator strain will eventually generaterandom mutations within the DNA.

The term “cassette mutagenesis” refers to any process for replacing asmall region of a double-stranded DNA molecule with a syntheticoligonucleotide “cassette” that differs from the native sequence. Theoligonucleotide often contains completely and/or partially randomizednative sequence.

The term “recursive ensemble mutagenesis” refers to an algorithm forprotein engineering (protein mutagenesis) developed to produce diversepopulations of phenotypically related mutants whose members differ inamino acid sequence. This method uses a feedback mechanism to controlsuccessive rounds of combinatorial cassette mutagenesis. See, e.g.,Arkin et al., Proc. Natl. Acad. Sci. U.S.A. 89: 7811-7815 (1992).

The term “exponential ensemble mutagenesis” refers to a process forgenerating combinatorial libraries with a high percentage of unique andfunctional mutants, wherein small groups of residues are randomized inparallel to identify, at each altered position, amino acids which leadto functional proteins. See, e.g., Delegrave et al., BiotechnologyResearch 11: 1548-1552 (1993); Arnold, Current Opinion in Biotechnology4: 450455 (1993).

“Operatively linked” expression control sequences refers to a linkage inwhich the expression control sequence is either contiguous with the geneof interest to control the gene of interest, or acts in trans or at adistance to control the gene of interest.

The term “expression control sequence” as used herein refers topolynucleotide sequences which are necessary to affect the expression ofcoding sequences to which they are operatively linked. Expressioncontrol sequences are sequences which control the transcription,post-transcriptional events and translation of nucleic acid sequences.Expression control sequences include appropriate transcriptioninitiation, termination, promoter and enhancer sequences; efficient RNAprocessing signals such as splicing and polyadenylation signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (e.g., ribosome binding sites); sequences thatenhance protein stability; and when desired, sequences that enhanceprotein secretion. The nature of such control sequences differsdepending upon the host organism; in prokaryotes, such control sequencesgenerally include promoter, ribosomal binding site, and transcriptiontermination sequence. The term “control sequences” is intended toinclude, at a minimum, all components whose presence is essential forexpression, and can also include additional components whose presence isadvantageous, for example, leader sequences and fusion partnersequences.

The term “vector,” as used herein, is intended to refer to a nucleicacid molecule capable of transporting another nucleic acid to which ithas been linked. One type of vector is a “plasmid”, which refers to acircular double-stranded DNA loop into which additional DNA segments maybe ligated. Other vectors include cosmids, bacterial artificialchromosomes (BAC) and yeast artificial chromosomes (YAC). Another typeof vector is a viral vector, wherein additional DNA segments may beligated into the viral genome. Viral vectors that infect bacterial cellsare referred to as bacteriophages. Certain vectors are capable ofautonomous replication in a host cell into which they are introduced(e.g., bacterial vectors having a bacterial origin of replication).Other vectors can be integrated into the genome of a host cell uponintroduction into the host cell, and thereby are replicated along withthe host genome. Moreover, certain vectors are capable of directing theexpression of genes to which they are operatively linked. Such vectorsare referred to herein as “recombinant expression vectors” (or simply,“expression vectors”). In general, expression vectors of utility inrecombinant DNA techniques are often in the form of plasmids. In thepresent specification, “plasmid” and “vector” may be usedinterchangeably as the plasmid is the most commonly used form of vector.However, the invention is intended to include other forms of expressionvectors that serve equivalent functions.

The term “recombinant host cell” (or simply “host cell”), as usedherein, is intended to refer to a cell into which a recombinantexpression vector has been introduced. It should be understood that suchterms are intended to refer not only to the particular subject cell butto the progeny of such a cell. Because certain modifications may occurin succeeding generations due to either mutation or environmentalinfluences, such progeny may not, in fact, be identical to the parentcell, but are still included within the scope of the term “host cell” asused herein.

As used herein, the phrase “open reading frame” and the equivalentacronym “ORF” refers to that portion of a transcript-derived nucleicacid that can be translated in its entirety into a sequence ofcontiguous amino acids. As so defined, an ORF has length, measured innucleotides, exactly divisible by 3. As so defined, an ORF need notencode the entirety of a natural protein.

As used herein, the phrase “ORF-encoded peptide” refers to the predictedor actual translation of an ORF.

As used herein, the phrase “degenerate variant” of a reference nucleicacid sequence is meant to be inclusive of all nucleic acid sequencesthat can be directly translated, using the standard genetic code, toprovide an amino acid sequence identical to that translated from thereference nucleic acid sequence.

The term “polypeptide” encompasses both naturally occurring andnon-naturally occurring proteins and polypeptides, as well aspolypeptide fragments and polypeptide mutants, derivatives and analogsthereof. A polypeptide may be monomeric or polymeric. Further, apolypeptide may comprise a number of different modules within a singlepolypeptide each of which has one or more distinct activities. Apreferred polypeptide in accordance with the invention comprises an OSPencoded by a nucleic acid molecule of the instant invention, or afragment, mutant, analog or derivative thereof.

The term “isolated protein” or “isolated polypeptide” is a protein orpolypeptide that by virtue of its origin or source of derivation (1) isnot associated with naturally associated components that accompany it inits native state, (2) is free of other proteins from the same species(3) is expressed by a cell from a different species, or (4) does notoccur in nature. Thus, a polypeptide that is chemically synthesized orsynthesized in a cellular system different from the cell from which itnaturally originates will be “isolated” from its naturally associatedcomponents. A polypeptide or protein may also be rendered substantiallyfree of naturally associated components by isolation, using proteinpurification techniques well known in the art.

A protein or polypeptide is “substantially pure,” “substantiallyhomogeneous” or “substantially purified” when at least about 60% to 75%of a sample exhibits a single species of polypeptide. The polypeptide orprotein may be monomeric or multimeric. A substantially pure polypeptideor protein will typically comprise about 50%, 60%, 70%, 80% or 90% W/Wof a protein sample, more usually about 95%, and preferably will be over99% pure. Protein purity or homogeneity may be determined by a number ofmeans well known in the art, such as polyacrylamide gel electrophoresisof a protein sample, followed by visualizing a single polypeptide bandupon staining the gel with a stain well known in the art. For certainpurposes, higher resolution may be provided by using HPLC or other meanswell known in the art for purification.

The term “fragment” when used herein with respect to polypeptides of thepresent invention refers to a polypeptide that has an amino-terminaland/or carboxy-terminal deletion compared to a full-length OSP. In apreferred embodiment, the fragment is a contiguous sequence in which theamino acid sequence of the fragment is identical to the correspondingpositions in the naturally occurring polypeptide. Fragments typicallyare at least 5, 6, 7, 8, 9 or 10 amino acids long, preferably at least12, 14, 16 or 18 amino acids long, more preferably at least 20 aminoacids long, more preferably at least 25, 30, 35, 40 or 45, amino acids,even more preferably at least 50 or 60 amino acids long, and even morepreferably at least 70 amino acids long.

A “derivative” when used herein with respect to polypeptides of thepresent invention refers to a polypeptide which is substantially similarin primary structural sequence to an OSP but which includes, e.g., invivo or in vitro chemical and biochemical modifications that are notfound in the OSP. Such modifications include, for example, acetylation,acylation, ADP-ribosylation, amidation, covalent attachment of flavin,covalent attachment of a heme moiety, covalent attachment of anucleotide or nucleotide derivative, covalent attachment of a lipid orlipid derivative, covalent attachment of phosphotidylinositol,cross-linking, cyclization, disulfide bond formation, demethylation,formation of covalent cross-links, formation of cystine, formation ofpyroglutamate, formylation, gamma-carboxylation, glycosylation, GPIanchor formation, hydroxylation, iodination, methylation,myristoylation, oxidation, proteolytic processing, phosphorylation,prenylation, racemization, selenoylation, sulfation, transfer-RNAmediated addition of amino acids to proteins such as arginylation, andubiquitination. Other modifications include, e.g., labeling withradionuclides, and various enzymatic modifications, as will be readilyappreciated by those skilled in the art. A variety of methods forlabeling polypeptides and of substituents or labels useful for suchpurposes are well known in the art, and include radioactive isotopessuch as ¹²⁵I, ³²P, ³⁵S, ¹⁴C and ³H, ligands which bind to labeledantiligands (e.g., antibodies), fluorophores, chemiluminescent agents,enzymes, and antiligands which can serve as specific binding pairmembers for a labeled ligand. The choice of label depends on thesensitivity required, ease of conjugation with the primer, stabilityrequirements, and available instrumentation. Methods for labelingpolypeptides are well known in the art. See Ausubel (1992), supra;Ausubel (1999), supra.

The term “fusion protein” refers to polypeptides of the presentinvention coupled to a heterologous amino acid sequence. Fusion proteinsare useful because they can be constructed to contain two or moredesired functional elements from two or more different proteins. Afusion protein comprises at least 10 contiguous amino acids from apolypeptide of interest, more preferably at least 20 or 30 amino acids,even more preferably at least 40, 50 or 60 amino acids, yet morepreferably at least 75, 100 or 125 amino acids. Fusion proteins can beproduced recombinantly by constructing a nucleic acid sequence thatencodes the polypeptide or a fragment thereof in frame with a nucleicacid sequence encoding a different protein or peptide and thenexpressing the fusion protein. Alternatively, a fusion protein can beproduced chemically by crosslinking the polypeptide or a fragmentthereof to another protein.

The term “analog” refers to both polypeptide analogs and non-peptideanalogs. The term “polypeptide analog” as used herein refers to apolypeptide that is comprised of a segment of at least 25 amino acidsthat has substantial identity to a portion of an amino acid sequence butwhich contains non-natural amino acids or non-natural inter-residuebonds. In a preferred embodiment, the analog has the same or similarbiological activity as the native polypeptide. Typically, polypeptideanalogs comprise a conservative amino acid substitution (or insertion ordeletion) with respect to the naturally occurring sequence. Analogstypically are at least 20 amino acids long, preferably at least 50 aminoacids long or longer, and can often be as long as a full-lengthnaturally occurring polypeptide.

The term “non-peptide analog” refers to a compound with properties thatare analogous to those of a reference polypeptide. A non-peptidecompound may also be termed a “peptide mimetic” or a “peptidomimetic.”Such compounds are often developed with the aid of computerizedmolecular modeling. Peptide mimetics that are structurally similar touseful peptides may be used to produce an equivalent effect. Generally,peptidomimetics are structurally similar to a paradigm polypeptide(i.e., a polypeptide that has a desired biochemical property orpharmacological activity), but have one or more peptide linkagesoptionally replaced by a linkage selected from the group consisting of:—CH₂NH—, —CH₂S—, —CH₂—CH₂—, —CH═CH-(cis and trans), —COCH₂—,—CH(OH)CH₂—, and —CH₂SO—, by methods well known in the art. Systematicsubstitution of one or more amino acids of a consensus sequence with aD-amino acid of the same type (e.g., D-lysine in place of L-lysine) mayalso be used to generate more stable peptides. In addition, constrainedpeptides comprising a consensus sequence or a substantially identicalconsensus sequence variation may be generated by methods known in theart (Rizo et al., Ann. Rev. Biochem. 61:387-418 (1992)). For example,one may add internal cysteine residues capable of forming intramoleculardisulfide bridges which cyclize the peptide.

The term “mutant” or “mutein” when referring to a polypeptide of thepresent invention relates to an amino acid sequence containingsubstitutions, insertions or deletions of one or more amino acidscompared to the amino acid sequence of an OSP. A mutein may have one ormore amino acid point substitutions, in which a single amino acid at aposition has been changed to another amino acid, one or more insertionsand/or deletions, in which one or more amino acids are inserted ordeleted, respectively, in the sequence of the naturally occurringprotein, and/or truncations of the amino acid sequence at either or boththe amino or carboxy termini. Further, a mutein may have the same ordifferent biological activity as the naturally occurring protein. Forinstance, a mutein may have an increased or decreased biologicalactivity. A mutein has at least 50% sequence similarity to the wild typeprotein, preferred is 60% sequence similarity, more preferred is 70%sequence similarity. Even more preferred are muteins having 80%, 85% or90% sequence similarity to an OSP. In an even more preferred embodiment,a mutein exhibits 95% sequence identity, even more preferably 97%, evenmore preferably 98% and even more preferably 99%. Sequence similaritymay be measured by any common sequence analysis algorithm, such as GAPor BESTFIT or other variation Smith-Waterman alignment. See, T. F. Smithand M. S. Waterman, J. Mol. Biol. 147:195-197 (1981) and W. R. Pearson,Genomics 11:635-650 (1991).

Preferred amino acid substitutions are those which: (1) reducesusceptibility to proteolysis, (2) reduce susceptibility to oxidation,(3) alter binding affinity for forming protein complexes, (4) alterbinding affinity or enzymatic activity, and (5) confer or modify otherphysicochemical or functional properties of such analogs. For example,single or multiple amino acid substitutions (preferably conservativeamino acid substitutions) may be made in the naturally occurringsequence (preferably in the portion of the polypeptide outside thedomain(s) forming intermolecular contacts. In a preferred embodiment,the amino acid substitutions are moderately conservative substitutionsor conservative substitutions. In a more preferred embodiment, the aminoacid substitutions are conservative substitutions. A conservative aminoacid substitution should not substantially change the structuralcharacteristics of the parent sequence (e.g., a replacement amino acidshould not tend to disrupt a helix that occurs in the parent sequence,or disrupt other types of secondary structure that characterize theparent sequence). Examples of art-recognized polypeptide secondary andtertiary structures are described in Creighton (ed.), Proteins,Structures and Molecular Principles, W. H. Freeman and Company (1984);Branden et al. (ed.), Introduction to Protein Structure, GarlandPublishing (1991); Thornton et al., Nature 354:105-106 (1991).

As used herein, the twenty conventional amino acids and theirabbreviations follow conventional usage. See Golub et al. (eds.),Immunology—A Synthesis 2^(nd) Ed., Sinauer Associates (1991).Stereoisomers (e.g., D-amino acids) of the twenty conventional aminoacids, unnatural amino acids such as α-, α-disubstituted amino acids,N-alkyl amino acids, and other unconventional amino acids may also besuitable components for polypeptides of the present invention. Examplesof unconventional amino acids include: 4-hydroxyproline,γ-carboxyglutamate, ε-N,N,N-trimethyllysine, ε-N-acetyllysine,O-phosphoserine, N-acetylserine, N-formylmethionine, ε-methylhistidine,5-hydroxylysine, s-N-methylarginine, and other similar amino acids andimino acids (e.g., 4-hydroxyproline). In the polypeptide notation usedherein, the lefthand direction is the amino terminal direction and theright hand direction is the carboxy-terminal direction, in accordancewith standard usage and convention.

By “homology” or “homologous” when referring to a polypeptide of thepresent invention it is meant polypeptides from different organisms witha similar sequence to the encoded amino acid sequence of an OSP and asimilar biological activity or function. Although two polypeptides aresaid to be “homologous,” this does not imply that there is necessarilyan evolutionary relationship between the polypeptides. Instead, the term“homologous” is defined to mean that the two polypeptides have similaramino acid sequences and similar biological activities or functions. Ina preferred embodiment, a homologous polypeptide is one that exhibits50% sequence similarity to OSP, preferred is 60% sequence similarity,more preferred is 70% sequence similarity. Even more preferred arehomologous polypeptides that exhibit 80%, 85% or 90% sequence similarityto an OSP. In yet a more preferred embodiment, a homologous polypeptideexhibits 95%, 97%, 98% or 99% sequence similarity.

When “sequence similarity” is used in reference to polypeptides, it isrecognized that residue positions that are not identical often differ byconservative amino acid substitutions. In a preferred embodiment, apolypeptide that has “sequence similarity” comprises conservative ormoderately conservative amino acid substitutions. A “conservative aminoacid substitution” is one in which an amino acid residue is substitutedby another amino acid residue having a side chain (R group) with similarchemical properties (e.g., charge or hydrophobicity). In general, aconservative amino acid substitution will not substantially change thefunctional properties of a protein. In cases where two or more aminoacid sequences differ from each other by conservative substitutions, thepercent sequence identity or degree of similarity may be adjustedupwards to correct for the conservative nature of the substitution.Means for making this adjustment are well known to those of skill in theart. See, e.g., Pearson, Methods Mol. Biol. 24: 307-31 (1994).

For instance, the following six groups each contain amino acids that areconservative substitutions for one another:

1) Serine (S), Threonine (T);

2) Aspartic Acid (D), Glutamic Acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Alanine (A), Valine (V),and

6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

Alternatively, a conservative replacement is any change having apositive value in the PAM250 log-likelihood matrix disclosed in Gonnetet al., Science 256: 1443-45 (1992). A “moderately conservative”replacement is any change having a nonnegative value in the PAM250log-likelihood matrix.

Sequence similarity for polypeptides, which is also referred to assequence identity, is typically measured using sequence analysissoftware. Protein analysis software matches similar sequences usingmeasures of similarity assigned to various substitutions, deletions andother modifications, including conservative amino acid substitutions.For instance, GCG contains programs such as “Gap” and “Bestfit” whichcan be used with default parameters to determine sequence homology orsequence identity between closely related polypeptides, such ashomologous polypeptides from different species of organisms or between awild type protein and a mutein thereof. See, e.g., GCG Version 6.1.Other programs include FASTA, discussed supra.

A preferred algorithm when comparing a sequence of the invention to adatabase containing a large number of sequences from different organismsis the computer program BLAST, especially blastp or tblastn. See, e.g.Altschul et al., J. Mol. Biol. 215: 403-410 (1990); Altschul et al.,Nucleic Acids Res. 25:3389-402 (1997). Preferred parameters for blastpare: Expectation value:  10 (default) Filter: seg (default) Cost to opena gap:  11 (default) Cost to extend a gap:  1 (default Max. alignments:100 (default) Word size:  11 (default) No. of descriptions: 100(default) Penalty Matrix: BLOSUM62

The length of polypeptide sequences compared for homology will generallybe at least about 16 amino acid residues, usually at least about 20residues, more usually at least about 24 residues, typically at leastabout 28 residues, and preferably more than about 35 residues. Whensearching a database containing sequences from a large number ofdifferent organisms, it is preferable to compare amino acid sequences.

Algorithms other than blastp for database searching using amino acidsequences are known in the art. For instance, polypeptide sequences canbe compared using FASTA, a program in GCG Version 6.1. FASTA (e.g.,FASTA2 and FASTA3) provides alignments and percent sequence identity ofthe regions of the best overlap between the query and search sequences(Pearson (1990), supra; Pearson (2000), supra. For example, percentsequence identity between amino acid sequences can be determined usingFASTA with its default or recommended parameters (a word size of 2 andthe PAM250 scoring matrix), as provided in GCG Version 6.1.

An “antibody” refers to an intact immunoglobulin, or to anantigen-binding portion thereof that competes with the intact antibodyfor specific binding to a molecular species, e.g., a polypeptide of theinstant invention. Antigen-binding portions may be produced byrecombinant DNA techniques or by enzymatic or chemical cleavage ofintact antibodies. Antigen-binding portions include, inter alia, Fab,Fab′, F(ab′)₂, Fv, dAb, and complementarity determining region (CDR)fragments, single-chain antibodies (scFv), chimeric antibodies,diabodies and polypeptides that contain at least a portion of animmunoglobulin that is sufficient to confer specific antigen binding tothe polypeptide. A Fab fragment is a monovalent fragment consisting ofthe VL, VH, CL and CH1 domains; a F(ab′)₂ fragment is a bivalentfragment comprising two Fab fragments linked by a disulfide bridge atthe hinge region; a Fd fragment consists of the VH and CH1 domains; a Fvfragment consists of the VL and VH domains of a single arm of anantibody; and a dAb fragment consists of a VH domain. See, e.g., Ward etal., Nature 341: 544-546 (1989).

By “bind specifically” and “specific binding” as used herein it is meantthe ability of the antibody to bind to a first molecular species inpreference to binding to other molecular species with which the antibodyand first molecular species are admixed. An antibody is said to“recognize” a first molecular species when it can bind specifically tothat first molecular species.

A single-chain antibody (scFv) is an antibody in which VL and VH regionsare paired to form a monovalent molecule via a synthetic linker thatenables them to be made as a single protein chain. See, e.g., Bird etal., Science 242: 423-426 (1988); Huston et al., Proc. Natl. Acad. Sci.USA 85: 5879-5883 (1988). Diabodies are bivalent, bispecific antibodiesin which VH and VL domains are expressed on a single polypeptide chain,but using a linker that is too short to allow for pairing between thetwo domains on the same chain, thereby forcing the domains to pair withcomplementary domains of another chain and creating two antigen bindingsites. See e.g., Holliger et al., Proc. Natl. Acad. Sci. USA 90:6444-6448 (1993); Poljak et al., Structure 2: 1121-1123 (1994). One ormore CDRs may be incorporated into a molecule either covalently ornoncovalently to make it an immunoadhesin. An immunoadhesin mayincorporate the CDR(s) as part of a larger polypeptide chain, maycovalently link the CDR(s) to another polypeptide chain, or mayincorporate the CDR(s) noncovalently. The CDRs permit the immunoadhesinto specifically bind to a particular antigen of interest. A chimericantibody is an antibody that contains one or more regions from oneantibody and one or more regions from one or more other antibodies.

An antibody may have one or more binding sites. If there is more thanone binding site, the binding sites may be identical to one another ormay be different. For instance, a naturally occurring immunoglobulin hastwo identical binding sites, a single-chain antibody or Fab fragment hasone binding site, while a “bispecific” or “bifunctional” antibody hastwo different binding sites.

An “isolated antibody” is an antibody that (1) is not associated withnaturally-associated components, including other naturally-associatedantibodies, that accompany it in its native state, (2) is free of otherproteins from the same species, (3) is expressed by a cell from adifferent species, or (4) does not occur in nature. It is known thatpurified proteins, including purified antibodies, may be stabilized withnon-naturally-associated components. The non-naturally-associatedcomponent may be a protein, such as albumin (e.g., BSA) or a chemicalsuch as polyethylene glycol (PEG).

A “neutralizing antibody” or “an inhibitory antibody” is an antibodythat inhibits the activity of a polypeptide or blocks the binding of apolypeptide to a ligand that normally binds to it. An “activatingantibody” is an antibody that increases the activity of a polypeptide.

The term “epitope” includes any protein determinant capable of specificbinding to an immunoglobulin or T-cell receptor. Epitopic determinantsusually consist of chemically active surface groupings of molecules suchas amino acids or sugar side chains and usually have specificthree-dimensional structural characteristics, as well as specific chargecharacteristics. An antibody is said to specifically bind an antigenwhen the dissociation constant is less than 1 μM, preferably less than100 nM and most preferably less than 10 nM.

The term “patient” includes human and veterinary subjects.

Throughout this specification and claims, the word “comprise,” orvariations such as “comprises” or “comprising,” will be understood toimply the inclusion of a stated integer or group of integers but not theexclusion of any other integer or group of integers.

The term “ovarian specific” refers to a nucleic acid molecule orpolypeptide that is expressed predominantly in the ovarian as comparedto other tissues in the body. In a preferred embodiment, a “ovarianspecific” nucleic acid molecule or polypeptide is detected at a levelthat is 1.5-fold higher than any other tissue in the body. In a morepreferred embodiment, the “ovarian specific” nucleic acid molecule orpolypeptide is detected at a level that is 2-fold higher than any othertissue in the body, more preferably 5-fold higher, still more preferablyat least 10-fold, 15-fold, 20-fold, 25-fold, 50-fold or 100-fold higherthan any other tissue in the body. Nucleic acid molecule levels may bemeasured by nucleic acid hybridization, such as Northern blothybridization, or quantitative PCR. Polypeptide levels may be measuredby any method known to accurately quantitate protein levels, such asWestern blot analysis.

Nucleic Acid Molecules, Regulatory Sequences, Vectors, Host Cells andRecombinant Methods of Making Polypeptides

Nucleic Acid Molecules

One aspect of the invention provides isolated nucleic acid moleculesthat are specific to the ovarian or to ovarian cells or tissue or thatare derived from such nucleic acid molecules. These isolated ovarianspecific nucleic acids (OSNAs) may comprise cDNA genomic DNA, RNA, or acombination thereof, a fragment of one of these nucleic acids, or may bea non-naturally occurring nucleic acid molecule. An OSNA may be derivedfrom an animal. In a preferred embodiment, the OSNA is derived from ahuman or other mammal. In a more preferred embodiment, the OSNA isderived from a human or other primate. In an even more preferredembodiment, the OSNA is derived from a human.

In a preferred embodiment, the nucleic acid molecule encodes apolypeptide that is specific to ovarian, an ovarian-specific polypeptide(OSP). In a more preferred embodiment, the nucleic acid molecule encodesa polypeptide that comprises an amino acid sequence of SEQ ID NO:129-295. In another highly preferred embodiment, the nucleic acidmolecule comprises a nucleic acid sequence of SEQ ID NO: 1-128.Nucleotide sequences of the instantly-described nucleic acid moleculeswere determined by assembling several DNA molecules from either publicor proprietary databases. Some of the underlying DNA sequences are theresult, directly or indirectly, of at least one enzymatic polymerizationreaction (e.g., reverse transcription and/or polymerase chain reaction)using an automated sequencer (such as the MegaBACE™ 1000, AmershamBiosciences, Sunnyvale, Calif., USA).

Nucleic acid molecules of the present invention may also comprisesequences that selectively hybridize to a nucleic acid molecule encodingan OSNA or a complement or antisense thereof The hybridizing nucleicacid molecule may or may not encode a polypeptide or may or may notencode an OSP. However, in a preferred embodiment, the hybridizingnucleic acid molecule encodes an OSP. In a more preferred embodiment,the invention provides a nucleic acid molecule that selectivelyhybridizes to a nucleic acid molecule or the antisense sequence of anucleic acid molecule that encodes a polypeptide comprising an aminoacid sequence of SEQ ID NO: 129-295. In an even more preferredembodiment, the invention provides a nucleic acid molecule thatselectively hybridizes to a nucleic acid molecule comprising the nucleicacid sequence of SEQ ID NO: 1-128 or the antisense sequence thereof.Preferably, the nucleic acid molecule selectively hybridizes to anucleic acid molecule or the antisense sequence of a nucleic acidmolecule encoding an OSP under low stringency conditions. Morepreferably, the nucleic acid molecule selectively hybridizes to anucleic acid molecule or the antisense sequence of a nucleic acidmolecule encoding an OSP under moderate stringency conditions. Mostpreferably, the nucleic acid molecule selectively hybridizes to anucleic acid molecule or the antisense sequence of a nucleic acidmolecule encoding an OSP under high stringency conditions. In apreferred embodiment, the nucleic acid molecule hybridizes under low,moderate or high stringency conditions to a nucleic acid molecule or theantisense sequence of a nucleic acid molecule encoding a polypeptidecomprising an amino acid sequence of SEQ ID NO: 129-295. In a morepreferred embodiment, the nucleic acid molecule hybridizes under low,moderate or high stringency conditions to a nucleic acid molecule or theantisense sequence of a nucleic acid molecule comprising a nucleic acidsequence selected from SEQ ID NO: 1-128.

Nucleic acid molecules of the present invention may also comprisenucleic acid sequences that exhibit substantial sequence similarity to anucleic acid encoding an OSP or a complement of the encoding nucleicacid molecule. In this embodiment, it is preferred that the nucleic acidmolecule exhibit substantial sequence similarity to a nucleic acidmolecule encoding human OSP. More preferred is a nucleic acid moleculeexhibiting substantial sequence similarity to a nucleic acid moleculeencoding a polypeptide having an amino acid sequence of SEQ ID NO:129-295. By substantial sequence similarity it is meant a nucleic acidmolecule having at least 60%, more preferably at least 70%, even morepreferably at least 80% and even more preferably at least 85% sequenceidentity with a nucleic acid molecule encoding an OSP, such as apolypeptide having an amino acid sequence of SEQ ID NO: 129-295. In amore preferred embodiment, the similar nucleic acid molecule is one thathas at least 90%, more preferably at least 95%, more preferably at least97%, even more preferably at least 98%, and still more preferably atleast 99% sequence identity with a nucleic acid molecule encoding anOSP. Most preferred in this embodiment is a nucleic acid molecule thathas at least 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity witha nucleic acid molecule encoding an OSP.

The nucleic acid molecules of the present invention are also inclusiveof those exhibiting substantial sequence similarity to an OSNA or itscomplement. In this embodiment, it is preferred that the nucleic acidmolecule exhibit substantial sequence similarity to a nucleic acidmolecule having a nucleic acid sequence of SEQ ID NO: 1-128. Bysubstantial sequence similarity it is meant a nucleic acid molecule thathas at least 60%, more preferably at least 70%, even more preferably atleast 80% and even more preferably at least 85% sequence identity withan OSNA, such as one having a nucleic acid sequence of SEQ ID NO: 1-128.More preferred is a nucleic acid molecule that has at least 90%, morepreferably at least 95%, more preferably at least 97%, even morepreferably at least 98%, and still more preferably at least 99% sequenceidentity with an OSNA. Most preferred is a nucleic acid molecule thathas at least 99.5%, 99.6%, 99.7%, 99.8% or 99.9% sequence identity withan OSNA.

Nucleic acid molecules that exhibit substantial sequence similarity areinclusive of sequences that exhibit sequence identity over their entirelength to an OSNA or to a nucleic acid molecule encoding an OSP, as wellas sequences that are similar over only a part of its length. In thiscase, the part is at least 50 nucleotides of the OSNA or the nucleicacid molecule encoding an OSP, preferably at least 100 nucleotides, morepreferably at least 150 or 200 nucleotides, even more preferably atleast 250 or 300 nucleotides, still more preferably at least 400 or 500nucleotides.

The substantially similar nucleic acid molecule may be a naturallyoccurring one that is derived from another species, especially onederived from another primate, wherein the similar nucleic acid moleculeencodes an amino acid sequence that exhibits significant sequenceidentity to that of SEQ ID NO: 129-295 or demonstrates significantsequence identity to the nucleotide sequence of SEQ ID NO: 1-128. Thesimilar nucleic acid molecule may also be a naturally occurring nucleicacid molecule from a human, when the OSNA is a member of a gene family.The similar nucleic acid molecule may also be a naturally occurringnucleic acid molecule derived from a non-primate, mammalian species,including without limitation, domesticated species, e.g., dog, cat,mouse, rat, rabbit, hamster, cow, horse and pig; and wild animals, e.g.,monkey, fox, lions, tigers, bears, giraffes, zebras, etc. Thesubstantially similar nucleic acid molecule may also be a naturallyoccurring nucleic acid molecule derived from a non-mammalian species,such as birds or reptiles. The naturally occurring substantially similarnucleic acid molecule may be isolated directly from humans or otherspecies. In another embodiment, the substantially similar nucleic acidmolecule may be one that is experimentally produced by random mutationof a nucleic acid molecule. In another embodiment, the substantiallysimilar nucleic acid molecule may be one that is experimentally producedby directed mutation of an OSNA. In a preferred embodiment, thesubstantially similar nucleic acid molecule is an OSNA.

The nucleic acid molecules of the present invention are also inclusiveof allelic variants of an OSNA or a nucleic acid encoding an OSP. Forexample, single nucleotide polymorphisms (SNPs) occur frequently ineukaryotic genomes and the sequence determined from one individual of aspecies may differ from other allelic forms present within thepopulation. More than 1.4 million SNPs have already been identified inthe human genome, International Human Genome Sequencing Consortium,Nature 409: 860-921 (2001)—Variants with small deletions and insertionsof more than a single nucleotide are also found in the generalpopulation, and often do not alter the function of the protein. Inaddition, amino acid substitutions occur frequently among naturalallelic variants, and often do not substantially change proteinfunction.

In a preferred embodiment, the allelic variant is a variant of a gene,wherein the gene is transcribed into a mRNA that encodes an OSP. In amore preferred embodiment, the gene is transcribed into a mRNA thatencodes an OSP comprising an amino acid sequence of SEQ ID NO: 129-295.In another preferred embodiment, the allelic variant is a variant of agene, wherein the gene is transcribed into a mRNA that is an OSNA. In amore preferred embodiment, the gene is transcribed into a mRNA thatcomprises the nucleic acid sequence of SEQ ID NO: 1-128. Also preferredis that the allelic variant be a naturally occurring allelic variant inthe species of interest, particularly human.

Nucleic acid molecules of the present invention are also inclusive ofnucleic acid sequences comprising a part of a nucleic acid sequence ofthe instant invention. The part may or may not encode a polypeptide, andmay or may not encode a polypeptide that is an OSP. In a preferredembodiment, the part encodes an OSP. In one embodiment, the nucleic acidmolecule comprises a part of an OSNA. In another embodiment, the nucleicacid molecule comprises a part of a nucleic acid molecule thathybridizes or exhibits substantial sequence similarity to an OSNA. Inanother embodiment, the nucleic acid molecule comprises a part of anucleic acid molecule that is an allelic variant of an OSNA. In yetanother embodiment, the nucleic acid molecule comprises a part of anucleic acid molecule that encodes an OSP. A part comprises at least 10nucleotides, more preferably at least 15, 17, 18, 20, 25, 30, 35, 40,50, 60, 70, 80, 90, 100, 150, 200, 250, 300, 350, 400 or 500nucleotides. The maximum size of a nucleic acid part is one nucleotideshorter than the sequence of the nucleic acid molecule encoding thefull-length protein.

Nucleic acid molecules of the present invention are also inclusive ofnucleic acid sequences that encode fusion proteins, homologous proteins,polypeptide fragments, muteins and polypeptide analogs, as describedinfra.

Nucleic acid molecules of the present invention are also inclusive ofnucleic acid sequences containing modifications of the native nucleicacid molecule. Examples of such modifications include, but are notlimited to, normative internucleoside bonds, post-syntheticmodifications or altered nucleotide analogues. One having ordinary skillin the art would recognize that the type of modification that may bemade will depend upon the intended use of the nucleic acid molecule. Forinstance, when the nucleic acid molecule is used as a hybridizationprobe, the range of such modifications will be limited to those thatpermit sequence-discriminating base pairing of the resulting nucleicacid. When used to direct expression of RNA or protein in vitro or invivo, the range of such modifications will be limited to those thatpermit the nucleic acid to function properly as a polymerizationsubstrate. When the isolated nucleic acid is used as a therapeuticagent, the modifications will be limited to those that do not confertoxicity upon the isolated nucleic acid.

Accordingly, in one embodiment, a nucleic acid molecule may includenucleotide analogues that incorporate labels that are directlydetectable, such as radiolabels or fluorophores, or nucleotide analoguesthat incorporate labels that can be visualized in a subsequent reaction,such as biotin or various haptens. The labeled nucleic acid moleculesare particularly useful as hybridization probes.

Common radiolabeled analogues include those labeled with ³³P, ³²P, and³⁵S, such as α-³²P-dATP, α-³²P-dCTP, α-³²P-dGTP, α-³²P-dTTP,α-³²P-3′dATP, α-³²P-ATP, α-³²P-CTP, α-³²P-GTP, α-³²P-UTP, α-³⁵S-dATP,γ-³⁵S-GTP, γ-³³P-dATP, and the like.

Commercially available fluorescent nucleotide analogues readilyincorporated into the nucleic acids of the present invention includeCy3-dCTP, Cy3-dUTP, Cy5-dCTP, Cy3-dUTP (Amersham Biosciences,Piscataway, N.J., USA), fluorescein-12-dUTP,tetramethylrhodamine-6-dUTP, Texas Red®-5-dUTP, Cascade Blue®-7-dUTP,BODIPY® FL-14-dUTP, BODIPY® TMR-14-dUTP, BODIPY® TR-14-dUTP, RhodamineGreen™-5-dUTP, Oregon Green® 488-5-dUTP, Texas Red®-12-dUTP, BODIPY®630/650-14-dUTP, BODIPY® 650/665-14-dUTP, Alexa Fluor® 488-5-dUTP, AlexaFluor® 532-5-dUTP, Alexa Fluor® 568-5-dUTP, Alexa Fluor® 594-5-dUTP,Alexa Fluor® 546-14-dUTP, fluorescein-12-UTP,tetramethylrhodamine-6-UTP, Texas Red®-5-UTP, Cascade Blue®-7-UTP,BODIPY® FL-14-UTP, BODIPY® TMR-14-UTP, BODIPY® TR-14-UTP, RhodamineGreen™-5-UTP, Alexa Fluor® 488-5-UTP, Alexa Fluor® 546-14-UTP (MolecularProbes, Inc. Eugene, Oreg., USA). One may also custom synthesizenucleotides having other fluorophores. See Henegariu et al., NatureBiotechnol. 18: 345-348 (2000).

Haptens that are commonly conjugated to nucleotides for subsequentlabeling include biotin (biotin-11-dUTP, Molecular Probes, Inc., Eugene,Oreg., USA; biotin-21-UTP, biotin-21-dUTP, Clontech Laboratories, Inc.,Palo Alto, Calif., USA), digoxigenin (DIG-11-dUTP, alkali labile,DIG-11-UTP, Roche Diagnostics Corp., Indianapolis, Ind., USA), anddinitrophenyl (dinitrophenyl-11-dUTP, Molecular Probes, Inc., Eugene,Oreg., USA).

Nucleic acid molecules of the present invention can be labeled byincorporation of labeled nucleotide analogues into the nucleic acid.Such analogues can be incorporated by enzymatic polymerization, such asby nick translation, random priming, polymerase chain reaction (PCR),terminal transferase tailing, and end-filling of overhangs, for DNAmolecules, and in vitro transcription driven, e.g., from phagepromoters, such as T7, T3, and SP6, for RNA molecules. Commercial kitsare readily available for each such labeling approach. Analogues canalso be incorporated during automated solid phase chemical synthesis.Labels can also be incorporated after nucleic acid synthesis, with the5′ phosphate and 3′ hydroxyl providing convenient sites forpost-synthetic covalent attachment of detectable labels.

Other post-synthetic approaches also permit internal labeling of nucleicacids. For example, fluorophores can be attached using a cisplatinreagent that reacts with the N7 of guanine residues (and, to a lesserextent, adenine bases) in DNA, RNA, and Peptide Nucleic Acids (PNA) toprovide a stable coordination complex between the nucleic acid andfluorophore label (Universal Linkage System) (available from MolecularProbes, Inc., Eugene, Oreg., USA and Amersham Pharmacia Biotech,Piscataway, N.J., USA); see Alers et al., Genes, Chromosomes & Cancer25: 301-305 (1999); Jelsma et al., J. NIH Res. 5: 82 (1994); Van Belkumet al., BioTechniques 16: 148-153 (1994). Alternatively, nucleic acidscan be labeled using a disulfide-containing linker (FastTag™ Reagent,Vector Laboratories, Inc., Burlingame, Calif., USA) that is photo- orthermally coupled to the target nucleic acid using aryl azide chemistry;after reduction, a free thiol is available for coupling to a hapten,fluorophore, sugar, affinity ligand, or other marker.

One or more independent or interacting labels can be incorporated intothe nucleic acid molecules of the present invention. For example, both afluorophore and a moiety that in proximity thereto acts to quenchfluorescence can be included to report specific hybridization throughrelease of fluorescence quenching or to report exonucleotidic excision.See, e.g., Tyagi et al., Nature Biotechnol. 14: 303-308 (1996); Tyagi etal., Nature Biotechnol. 16: 49-53 (1998); Sokol et al., Proc. Natl.Acad. Sci. USA 95: 11538-11543 (1998); Kostrikis et al., Science 279:1228-1229 (1998); Marras et al., Genet. Anal. 14: 151-156 (1999);Holland et al., Proc. Natl. Acad. Sci. USA 88: 7276-7280 (1991); Heid etal., Genome Res. 6(10): 986-94 (1996); Kuimelis et al., Nucleic AcidsSymp. Ser. (37): 255-6 (1997); and U.S. Pat. Nos. 5,846,726, 5,925,517,5,925,517, 5,723,591 and 5,538,848, the disclosures of which areincorporated herein by reference in their entireties.

Nucleic acid molecules of the present invention may also be modified byaltering one or more native phosphodiester internucleoside bonds to morenuclease-resistant, internucleoside bonds. See Hartmann et al. (eds.),Manual of Antisense Methodology; Perspectives in Antisense Science,Kluwer Law International (1999); Stein et al. (eds.), Applied AntisenseOligonucleotide Technology, Wiley-Liss (1998); Chadwick et al. (eds.),Oligonucleotides as Therapeutic Agents—Symposium No. 209, John Wiley &Son Ltd (1997). Such altered internucleoside bonds are often desired fortechniques or for targeted gene correction, Gamper et al., Nucl. AcidsRes. 28(21): 4332-4339 (2000). For double-stranded RNA inhibition whichmay utilize either natural ds RNA or ds RNA modified in its, sugar,phosphate or base, see Hannon, Nature 418(11): 244-251 (2002); Fire etal. in WO 99/32619; Tuschl et al. in US2002/0086356; Kruetzer et al. inWO 00/44895, the disclosures of which are incorporated herein byreference in their entirety. For circular antisense, see Kool in U.S.Pat. No. 5,426,180, the disclosure of which is incorporated herein byreference in its entirety.

Modified oligonucleotide backbones include, without limitation,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl and other alkylphosphonates including 3′-alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′.Representative U.S. Patents that teach the preparation of the abovephosphorus-containing linkages include, but are not limited to, U.S.Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;5,587,361; and 5,625,050, the disclosures of which are incorporatedherein by reference in their entireties. In a preferred embodiment, themodified internucleoside linkages may be used for antisense techniques.

Other modified oligonucleotide backbones do not include a phosphorusatom, but have backbones that are formed by short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These includethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH₂ component parts. Representative U.S. patents that teach thepreparation of the above backbones include, but are not limited to, U.S.Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141;5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677;5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240;5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070;5,663,312; 5,633,360; 5,677,437 and 5,677,439; the disclosures of whichare incorporated herein by reference in their entireties.

In other preferred nucleic acid molecules, both the sugar and theinternucleoside linkage are replaced with novel groups, such as peptidenucleic acids (PNA). In PNA compounds, the phosphodiester backbone ofthe nucleic acid is replaced with an amide-containing backbone, inparticular by repeating N-(2-aminoethyl) glycine units linked by amidebonds. Nucleobases are bound directly or indirectly to aza nitrogenatoms of the amide portion of the backbone, typically by methylenecarbonyl linkages. PNA can be synthesized using a modified peptidesynthesis protocol. PNA oligomers can be synthesized by both Fmoc andtBoc methods. Representative U.S. patents that teach the preparation ofPNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082;5,714,331; and 5,719,262, each of which is herein incorporated byreference in its entirety. Automated PNA synthesis is readily achievableon commercial synthesizers (see, e.g., “PNA User's Guide,” Rev. 2,February 1998, Perseptive Biosystems Part No. 60138, Applied Biosystems,Inc., Foster City, Calif.). PNA molecules are advantageous for a numberof reasons. First, because the PNA backbone is uncharged, PNA/DNA andPNA/RNA duplexes have a higher thermal stability than is found inDNA/DNA and DNA/RNA duplexes. The Tm of a PNA/DNA or PNA/RNA duplex isgenerally 1° C. higher per base pair than the Tm of the correspondingDNA/DNA or DNA/RNA duplex (in 100 mM NaCl). Second, PNA molecules canalso form stable PNA/DNA complexes at low ionic strength, underconditions in which DNA/DNA duplex formation does not occur. Third, PNAalso demonstrates greater specificity in binding to complementary DNAbecause a PNA/DNA mismatch is more destabilizing than DNA/DNA mismatch.A single mismatch in mixed a PNA/DNA 15-mer lowers the Tm by 8-20° C.(15° C. on average). In the corresponding DNA/DNA duplexes, a singlemismatch lowers the Tm by 4-16° C. (11° C. on average). Because PNAprobes can be significantly shorter than DNA probes, their specificityis greater. Fourth, PNA oligomers are resistant to degradation byenzymes, and the lifetime of these compounds is extended both in vivoand in vitro because nucleases and proteases do not recognize the PNApolyamide backbone with nucleobase sidechains. See, e.g., Ray et al.,FASEB J. 14(9): 1041-60 (2000); Nielsen et al., Pharmacol Toxicol.86(1): 3-7 (2000); Larsen et al., Biochim Biophys Acta. 1489(1): 159-66(1999); Nielsen, Curr. Opin. Struct. Biol. 9(3): 353-7 (1999), andNielsen, Curr. Opin. Biotechnol. 10(1): 71-5 (1999).

Nucleic acid molecules may be modified compared to their nativestructure throughout the length of the nucleic acid molecule or can belocalized to discrete portions thereof. As an example of the latter,chimeric nucleic acids can be synthesized that have discrete DNA and RNAdomains and that can be used for targeted gene repair and modified PCRreactions, as further described in, Misra et al., Biochem. 37: 1917-1925(1998); and Finn et al., Nucl. Acids Res. 24: 3357-3363 (1996), and U.S.Pat. Nos. 5,760,012 and 5,731,181, the disclosures of which areincorporated herein by reference in their entireties.

Unless otherwise specified, nucleic acid molecules of the presentinvention can include any topological conformation appropriate to thedesired use; the term thus explicitly comprehends, among others,single-stranded, double-stranded, triplexed, quadruplexed, partiallydouble-stranded, partially-triplexed, partially-quadruplexed, branched,hairpinned, circular, and padlocked conformations. Padlockedconformations and their utilities are further described in Banér et al.,Curr. Opin. Biotechnol. 12: 11-15 (2001); Escude et al., Proc. Natl.Acad. Sci. USA 14: 96(19):10603-7 (1999); and Nilsson et al., Science265(5181): 2085-8 (1994). Triplexed and quadruplexed conformations, andtheir utilities, are reviewed in Praseuth et al., Biochim. Biophys.Acta. 1489(1): 181-206 (1999); Fox, Curr. Med. Chem. 7(1): 17-37 (2000);Kochetkova et al., Methods Mol. Biol. 130: 189-201 (2000); Chan et al.,J. Mol. Med. 75(4): 267-82 (1997); Rowley et al., Mol Med 5(10): 693-700(1999); Kool, Annu Rev Biophys Biomol Struct. 25: 1-28 (1996).

SNP Polymorphisms

Commonly, sequence differences between individuals involve differencesin single nucleotide positions. SNPs may account for 90% of human DNApolymorphism. Collins et al., 8 Genome Res. 1229-31 (1998). SNPs includesingle base pair positions in genomic DNA at which different sequencealternatives (alleles) exist in a population. In addition, the leastfrequent allele generally must occur at a frequency of 1% or greater.DNA sequence variants with a reasonably high population frequency areobserved approximately every 1,000 nucleotide across the genome, withestimates as high as 1 SNP per 350 base pairs. Wang et al., 280 Science1077-82 (1998); Harding et al, 60 Am. J. Human Genet. 772-89 (1997);Taillon-Miller et al., 8 Genome Res. 748-54 (1998); Cargill et al., 22Nat. Genet. 231-38 (1999); and Semple et al., 16 Bioinform. Disc. Note735-38 (2000). The frequency of SNPs varies with the type and locationof the change. In base substitutions, two-thirds of the substitutionsinvolve the C-T and G-A type. This variation in frequency can be relatedto 5-methylcytosine deamination reactions that occur frequently,particularly at CpG dinucleotides. Regarding location, SNPs occur at amuch higher frequency in non-coding regions than in coding regions.Information on over one million variable sequences is already publiclyavailable via the Internet and more such markers are available fromcommercial providers of genetic information. Kwok and Gu, 5 Med. Today538-53 (1999).

Several definitions of SNPs exist See, e.g., Brooks, 235 Gene 177-86(1999). As used herein, the term “single nucleotide polymorphism” or“SNP” includes all single base variants, thus including nucleotideinsertions and deletions in addition to single nucleotide substitutions.There are two types of nucleotide substitutions. A transition is thereplacement of one purine by another purine or one pyrimidine by anotherpyrimidine. A transversion is the replacement of a purine for apyrimidine, or vice versa.

Numerous methods exist for detecting SNPs within a nucleotide sequence.A review of many of these methods can be found in Landegren et al., 8Genome Res. 769-76 (1998). For example, a SNP in a genomic sample can bedetected by preparing a Reduced Complexity Genome (RCG) from the genomicsample, then analyzing the RCG for the presence or absence of a SNP.See, e.g., WO 00/18960 which is herein incorporated by reference in itsentirety. Multiple SNPs in a population of target polynucleotides inparallel can be detected using, for example, the methods of WO 00/50869which is herein incorporated by reference in its entirety. Other SNPdetection methods include the methods of U.S. Pat. Nos. 6,297,018 and6,322,980 which are herein incorporated by reference in their entirety.Furthermore, SNPs can be detected by restriction fragment lengthpolymorphism (RFLP) analysis. See, e.g., U.S. Pat. Nos. 5,324,631;5,645,995 which are herein incorporated by reference in their entirety.RFLP analysis of SNPs, however, is limited to cases where the SNP eithercreates or destroys a restriction enzyme cleavage site. SNPs can also bedetected by direct sequencing of the nucleotide sequence of interest. Inaddition, numerous assays based on hybridization have also beendeveloped to detect SNPs and mismatch distinction by polymerases andligases. Several web sites provide information about SNPs includingEnsembl on the World Wide Web at ensemble.org, Sanger Institute on theWorld Wide Web at sanger.ac.uk/genetics/exon/, National Center forBiotechnology Information (NCBI) on the World Wide Web atncbi.nlm.nih.gov/SNP/, The SNP Consortium Ltd. on the World Wide Web atsnp.cshl.org. The chromosomal locations for the compositions disclosedherein are provided below. In addition, one of ordinary skill in the artcould use a BLAST against the genome or any of the databases cited aboveto find the chromosomal location. Another a preferred method to find thegenomic coordinates and associated SNPs would be to use the BLAT tool(genome.ucsc.edu, Kent et al. 2001, The Human Genome Browser at UCSC,Genome Research 996-1006 or Kent 2002 BLAT—The BLAST-Like Alignment ToolGenome Research, 1-9 ). All web sites above were accessed Dec. 3, 2003.

RNA Interference

RNA interference refers to the process of sequence-specific posttranscriptional gene silencing in animals mediated by short interferingRNAs (siRNA). Fire et al., 1998, Nature, 391, 806. The correspondingprocess in plants is commonly referred to as post transcriptional genesilencing or RNA silencing and is also referred to as quelling in fungi.The process of post transcriptional gene silencing is thought to be anevolutionarily conserved cellular defense mechanism used to prevent theexpression of foreign genes which is commonly shared by diverse floraand phyla. Fire et al., 1999, Trends Genet., 15, 358. Such protectionfrom foreign gene expression may have evolved in response to theproduction of double-stranded RNAs (dsRNA) derived from viral infectionor the random integration of transposon elements into a host genome viaa cellular response that specifically destroys homologoussingle-stranded RNA or viral genomic RNA. The presence of dsRNA in cellstriggers the RNAi response though a mechanism that has yet to be fullycharacterized. This mechanism appears to be different from theinterferon response that results from dsRNA mediated activation ofprotein kinase PKR and 2′,5′-oligoadenylate synthetase resulting innon-specific cleavage of mRNA by ribonuclease L.

The presence of long dsRNAs in cells stimulates the activity of aribonuclease III enzyme referred to as dicer. Dicer is involved in theprocessing of the dsRNA into short pieces of dsRNA known as shortinterfering RNAs (siRNA). Berstein et al., 2001, Nature, 409, 363. Shortinterfering RNAs derived from dicer activity are typically about 21-23nucleotides in length and comprise about 19 base pair duplexes. Dicerhas also been implicated in the excision of 21 and 22 nucleotide smalltemporal RNAs (stRNA) from precursor RNA of conserved structure that areimplicated in translational control. Hutvagner et al., 2001, Science,293, 834. The RNAi response also features an endonuclease complexcontaining a siRNA, commonly referred to as an RNA-induced silencingcomplex (RISC), which mediates cleavage of single-stranded RNA havingsequence complementary to the antisense strand of the siRNA duplex.Cleavage of the target RNA takes place in the middle of the regioncomplementary to the antisense strand of the siRNA duplex. Elbashir etal., 2001, Genes Dev., 15, 188.

Short interfering RNA mediated RNAi has been studied in a variety ofsystems. Fire et al., 1998, Nature, 391, 806, were the first to observeRNAi in C. Elegans. Wianny and Goetz, 1999, Nature Cell Biol., 2, 70,describe RNAi mediated by dsRNA in mouse embryos. Hammond et al., 2000,Nature, 404, 293, describe RNAi in Drosophila cells transfected withdsRNA. Elbashir et al., 2001, Nature, 411, 494, describe RNAi induced byintroduction of duplexes of synthetic 21-nucleotide RNAs in culturedmammalian cells including human embryonic kidney and HeLa cells. Recentwork in Drosophila embryonic lysates (Elbashir et al., 2001, EMBO J.,20, 6877) has revealed certain requirements for siRNA length, structure,chemical composition, and sequence that are essential to mediateefficient RNAi activity. These studies have shown that 21 nucleotidesiRNA duplexes are most active when containing two nucleotide3′-overhangs. Furthermore, complete substitution of one or both siRNAstrands with 2′-deoxy (2′-H) or 2′-O-methyl nucleotides abolishes RNAiactivity, whereas substitution of the 3′-terminal siRNA overhangnucleotides with deoxy nucleotides (2′-H) was shown to be tolerated.Single mismatch sequences in the center of the siRNA duplex were alsoshown to abolish RNAi activity. In addition, these studies also indicatethat the position of the cleavage site in the target RNA is defined bythe 5′-end of the siRNA guide sequence rather than the 3′-end. Elbashiret al., 2001, EMBO J., 20, 6877. Other studies have indicated that a5′-phosphate on the target-complementary strand of a siRNA duplex isrequired for siRNA activity and that ATP is utilized to maintain the5′-phosphate moiety on the siRNA. Nykanen et al., 2001, Cell, 107, 309.

Studies have shown that replacing the 3′-overhanging segments of a21-mer siRNA duplex having 2 nucleotide 3′ overhangs withdeoxyribonucleotides does not have an adverse effect on RNAi activity.Replacing up to 4 nucleotides on each end of the siRNA withdeoxyribonucleotides has been reported to be well tolerated whereascomplete substitution with deoxyribonucleotides results in no RNAiactivity. Elbashir et al., 2001, EMBO J., 20, 6877. In addition,Elbashir et al., supra, also report that substitution of siRNA with2′-O-methyl nucleotides completely abolishes RNAi activity. Li et al.,WO 00/44914, and Beach et al., WO 01/68836 both suggest that siRNA “mayinclude modifications to either the phosphate-sugar back bone or thenucleoside to include at least one of a nitrogen or sulfur heteroatom”,however neither application teaches to what extent these modificationsare tolerated in siRNA molecules nor provides any examples of suchmodified siRNA. Kreutzer and Limmer, Canadian Patent Application No.2,359,180, also describe certain chemical modifications for use in dsRNAconstructs in order to counteract activation of double-strandedRNA-dependent protein kinase PKR, specifically 2′-amino or 2′-O-methylnucleotides, and nucleotides containing a 2′-O or 4′-C methylene bridge.However, Kreutzer and Limmer similarly fail to show to what extent thesemodifications are tolerated in siRNA molecules nor do they provide anyexamples of such modified siRNA.

Parrish et al., 2000, Molecular Cell, 6, 1977-1087, tested certainchemical modifications targeting the unc-22 gene in C. elegans usinglong (>25 nt) siRNA transcripts. The authors describe the introductionof thiophosphate residues into these siRNA transcripts by incorporatingthiophosphate nucleotide analogs with T7 and T3 RNA polymerase andobserved that “RNAs with two [phosphorothioate] modified bases also hadsubstantial decreases in effectiveness as RNAi triggers;[phosphorothioate] modification of more than two residues greatlydestabilized the RNAs in vitro and we were not able to assayinterference activities.” Parrish et al. at 1081. The authors alsotested certain modifications at the 2′-position of the nucleotide sugarin the long siRNA transcripts and observed that substitutingdeoxynucleotides for ribonucleotides “produced a substantial decrease ininterference activity”, especially in the case of Uridine to Thymidineand/or Cytidine to deoxy-Cytidine substitutions. Parrish et al. Inaddition, the authors tested certain base modifications, includingsubstituting 4-thiouracil, 5-bromouracil, 5-iodouracil,3-(aminoallyl)uracil for uracil, and inosine for guanosine in sense andantisense strands of the siRNA, and found that whereas 4-thiouracil and5-bromouracil were all well tolerated, inosine “produced a substantialdecrease in interference activity” when incorporated in either strand.Incorporation of 5-iodouracil and 3-(aminoallyl)uracil in the antisensestrand resulted in substantial decrease in RNAi activity as well.

Beach et al., WO 01/68836, describes specific methods for attenuatinggene expression using endogenously derived dsRNA. Tuschl et al., WO01/75164, describes a Drosophila in vitro RNAi system and the use ofspecific siRNA molecules for certain functional genomic and certaintherapeutic applications; although Tuschl, 2001, Chem. Biochem., 2,239-245, doubts that RNAi can be used to cure genetic diseases or viralinfection due “to the danger of activating interferon response”. Li etal., WO 00/44914, describes the use of specific dsRNAs for use inattenuating the expression of certain target genes. Zernicka-Goetz etal., WO 01/36646, describes certain methods for inhibiting theexpression of particular genes in mammalian cells using certain dsRNAmolecules. Fire et al., WO 99/32619, U.S. Pat. No. 6,506,559, thecontents of which are hereby incorporated by reference in theirentirety, describes particular methods for introducing certain dsRNAmolecules into cells for use in inhibiting gene expression. Plaetinck etal., WO 00/01846, describes certain methods for identifying specificgenes responsible for conferring a particular phenotype in a cell usingspecific dsRNA molecules. Mello et al., WO 01/29058, describes theidentification of specific genes involved in dsRNA mediated RNAi.Deschamps Depaillette et al., International PCT Publication No. WO99/07409, describes specific compositions consisting of particular dsRNAmolecules combined with certain anti-viral agents. Driscoll et al.,International PCT Publication No. WO 01/49844, describes specific DNAconstructs for use in facilitating gene silencing in targeted organisms.Parrish et al., 2000, Molecular Cell, 6, 1977-1087, describes specificchemically modified siRNA constructs targeting the unc-22 gene of C.elegans. Tuschl et al., International PCT Publication No. WO 02/44321,describe certain synthetic siRNA constructs.

Methods for Using Nucleic Acid Molecules as Probes and Primers

The isolated nucleic acid molecules of the present invention can be usedas hybridization probes to detect, characterize, and quantifyhybridizing nucleic acids in, and isolate hybridizing nucleic acidsfrom, both genomic and transcript-derived nucleic acid samples. Whenfree in solution, such probes are typically, but not invariably,detectably labeled; bound to a substrate, as in a microarray, suchprobes are typically, but not invariably unlabeled.

In one embodiment, the isolated nucleic acid molecules of the presentinvention can be used as probes to detect and characterize grossalterations in the gene of an OSNA, such as deletions, insertions,translocations, and duplications of the OSNA genomic locus throughfluorescence in situ hybridization (FISH) to chromosome spreads. See,e.g., Andreeff et al. (eds.), Introduction to Fluorescence In SituHybridization: Principles and Clinical Applications, John Wiley & Sons(1999). The isolated nucleic acid molecules of the present invention canbe used as probes to assess smaller genomic alterations using, e.g.,Southern blot detection of restriction fragment length polymorphisms.The isolated nucleic acid molecules of the present invention can be usedas probes to isolate genomic clones that include a nucleic acid moleculeof the present invention, which thereafter can be restriction mapped andsequenced to identify deletions, insertions, translocations, andsubstitutions (single nucleotide polymorphisms, SNPs) at the sequencelevel. Alternatively, detection techniques such as molecular beacons maybe used, see Kostrikis et al. Science 279:1228-1229 (1998).

The isolated nucleic acid molecules of the present invention can also beused as probes to detect, characterize, and quantify OSNA in, andisolate OSNA from, transcript-derived nucleic acid samples. In oneembodiment, the isolated nucleic acid molecules of the present inventioncan be used as hybridization probes to detect, characterize by length,and quantify mRNA by Northern blot of total or poly-A⁺-selected RNAsamples. In another embodiment, the isolated nucleic acid molecules ofthe present invention can be used as hybridization probes to detect,characterize by location, and quantify mRNA by in situ hybridization totissue sections. See, e.g., Schwarchzacher et al., In SituHybridization. Springer-Verlag New York (2000). In another preferredembodiment, the isolated nucleic acid molecules of the present inventioncan be used as hybridization probes to measure the representation ofclones in a cDNA library or to isolate hybridizing nucleic acidmolecules acids from cDNA libraries, permitting sequence levelcharacterization of mRNAs that hybridize to OSNAs, including, withoutlimitations, identification of deletions, insertions, substitutions,truncations, alternatively spliced forms and single nucleotidepolymorphisms. In yet another preferred embodiment, the nucleic acidmolecules of the instant invention may be used in microarrays.

All of the aforementioned probe techniques are well within the skill inthe art, and are described at greater length in standard texts such asSambrook (2001), supra; Ausubel (1999), supra; and Walker et al. (eds.),The Nucleic Acids Protocols Handbook, Humana Press (2000).

In another embodiment, a nucleic acid molecule of the invention may beused as a probe or primer to identify and/or amplify a second nucleicacid molecule that selectively hybridizes to the nucleic acid moleculeof the invention. In this embodiment, it is preferred that the probe orprimer be derived from a nucleic acid molecule encoding an OSP. Morepreferably, the probe or primer is derived from a nucleic acid moleculeencoding a polypeptide having an amino acid sequence of SEQ ID NO:129-295. Also preferred are probes or primers derived from an OSNA. Morepreferred are probes or primers derived from a nucleic acid moleculehaving a nucleotide sequence of SEQ ID NO: 1-128.

In general, a probe or primer is at least 10 nucleotides in length, morepreferably at least 12, more preferably at least 14 and even morepreferably at least 16 or 17 nucleotides in length. In an even morepreferred embodiment, the probe or primer is at least 18 nucleotides inlength, even more preferably at least 20 nucleotides and even morepreferably at least 22 nucleotides in length. Primers and probes mayalso be longer in length. For instance, a probe or primer may be 25nucleotides in length, or may be 30, 40 or 50 nucleotides in length.Methods of performing nucleic acid hybridization using oligonucleotideprobes are well known in the art. See, e.g., Sambrook et al., 1989,supra, Chapter 11 and pp. 11.31-11.32 and 11.40-11.44, which describesradiolabeling of short probes, and pp. 11.45-11.53, which describehybridization conditions for oligonucleotide probes, including specificconditions for probe hybridization (pp. 11.50-11.51).

Methods of performing primer-directed amplification are also well knownin the art. Methods for performing the polymerase chain reaction (PCR)are compiled, inter alia, in McPherson, PCR Basics: From Background toBench, Springer Verlag (2000); Innis et al. (eds.), PCR Applications:Protocols for Functional Genomics, Academic Press (1999); Gelfand et al.(eds.), PCR Strategies, Academic Press (1998); Newton et al., PCR,Springer-Verlag New York (1997); Burke (ed.), PCR: Essential Techniques,John Wiley & Son Ltd (1996); White (ed.), PCR Cloning Protocols: FromMolecular Cloning to Genetic Engineering, Vol. 67, Humana Press (1996);and McPherson et al. (eds.), PCR 2: A Practical Approach, OxfordUniversity Press, Inc. (1995). Methods for performing RT-PCR arecollected, e.g., in Siebert et al. (eds.), Gene Cloning and Analysis byRT-PCR, Eaton Publishing Company/Bio Techniques Books Division, 1998;and Siebert (ed.), PCR Technique:RT-PCR, Eaton PublishingCompany/BioTechniques Books (1995).

PCR and hybridization methods may be used to identify and/or isolatenucleic acid molecules of the present invention including allelicvariants, homologous nucleic acid molecules and fragments. PCR andhybridization methods may also be used to identify, amplify and/orisolate nucleic acid molecules of the present invention that encodehomologous proteins, analogs, fusion proteins or muteins of theinvention. Nucleic acid primers as described herein can be used to primeamplification of nucleic acid molecules of the invention, usingtranscript-derived or genomic DNA as the template.

These nucleic acid primers can also be used, for example, to primesingle base extension (SBE) for SNP detection (See, e.g., U.S. Pat. No.6,004,744, the disclosure of which is incorporated herein by referencein its entirety).

Isothermal amplification approaches, such as rolling circleamplification, are also now well-described. See, e.g., Schweitzer etal., Curr. Opin. Biotechnol. 12(1): 21-7 (2001); International Patentpublications WO 97/19193 and WO 00/15779, and U.S. Pat. Nos. 5,854,033and 5,714,320, the disclosures of which are incorporated herein byreference in their entireties. Rolling circle amplification can becombined with other techniques to facilitate SNP detection. See, e.g.,Lizardi et al., Nature Genet. 19(3): 225-32 (1998).

Nucleic acid molecules of the present invention may be bound to asubstrate either covalently or noncovalently. The substrate can beporous or solid, planar or non-planar, unitary or distributed. The boundnucleic acid molecules may be used as hybridization probes, and may belabeled or unlabeled. In a preferred embodiment, the bound nucleic acidmolecules are unlabeled.

In one embodiment, the nucleic acid molecule of the present invention isbound to a porous substrate, e.g., a membrane, typically comprisingnitrocellulose, nylon, or positively charged derivatized nylon. Thenucleic acid molecule of the present invention can be used to detect ahybridizing nucleic acid molecule that is present within a labelednucleic acid sample, e.g., a sample of transcript-derived nucleic acids.In another embodiment, the nucleic acid molecule is bound to a solidsubstrate, including, without limitation, glass, amorphous silicon,crystalline silicon or plastics. Examples of plastics include, withoutlimitation, polymethylacrylic, polyethylene, polypropylene,polyacrylate, polymethylmethacrylate, polyvinylchloride,polytetrafluoroethylene, polystyrene, polycarbonate, polyacetal,polysulfone, celluloseacetate, cellulosenitrate, nitrocellulose, ormixtures thereof. The solid substrate may be any shape, includingrectangular, disk-like and spherical. In a preferred embodiment, thesolid substrate is a microscope slide or slide-shaped substrate.

The nucleic acid molecule of the present invention can be attachedcovalently to a surface of the support substrate or applied to aderivatized surface in a chaotropic agent that facilitates denaturationand adherence by presumed noncovalent interactions, or some combinationthereof. The nucleic acid molecule of the present invention can be boundto a substrate to which a plurality of other nucleic acids areconcurrently bound, hybridization to each of the plurality of boundnucleic acids being separately detectable. At low density, e.g. on aporous membrane, these substrate-bound collections are typicallydenominated macroarrays; at higher density, typically on a solidsupport, such as glass, these substrate bound collections of pluralnucleic acids are colloquially termed microarrays. As used herein, theterm microarray includes arrays of all densities. It is, therefore,another aspect of the invention to provide microarrays that comprise oneor more of the nucleic acid molecules of the present invention.

In yet another embodiment, the invention is directed to single exonprobes based on the OSNAs disclosed herein.

Expression Vectors, Host Cells and Recombinant Methods of ProducingPolypeptides

Another aspect of the present invention provides vectors that compriseone or more of the isolated nucleic acid molecules of the presentinvention, and host cells in which such vectors have been introduced.

The vectors can be used, inter alia, for propagating the nucleic acidmolecules of the present invention in host cells (cloning vectors), forshuttling the nucleic acid molecules of the present invention betweenhost cells derived from disparate organisms (shuttle vectors), forinserting the nucleic acid molecules of the present invention into hostcell chromosomes (insertion vectors), for expressing sense or antisenseRNA transcripts of the nucleic acid molecules of the present inventionin vitro or within a host cell, and for expressing polypeptides encodedby the nucleic acid molecules of the present invention, alone or asfusion proteins with heterologous polypeptides (expression vectors).Vectors are by now well known in the art, and are described, inter alia,in Jones et al. (eds.), Vectors: Cloning Applications: EssentialTechniques (Essential Techniques Series), John Wiley & Son Ltd. (1998);Jones et al. (eds.), Vectors: Expression Systems: Essential Techniques(Essential Techniques Series), John Wiley & Son Ltd. (1998); Gacesa etal., Vectors: Essential Data, John Wiley & Sons Ltd. (1995); Cid-Arregui(eds.), Viral Vectors: Basic Science and Gene Therapy, Eaton PublishingCo. (2000); Sambrook (2001), supra; Ausubel (1999), supra. Furthermore,a variety of vectors are available commercially. Use of existing vectorsand modifications thereof are well within the skill in the art. Thus,only basic features need be described here.

Nucleic acid sequences may be expressed by operatively linking them toan expression control sequence in an appropriate expression vector andemploying that expression vector to transform an appropriate unicellularhost. Expression control sequences are sequences that control thetranscription, post-transcriptional events and translation of nucleicacid sequences. Such operative linking of a nucleic acid sequence ofthis invention to an expression control sequence, of course, includes,if not already part of the nucleic acid sequence, the provision of atranslation initiation codon, ATG or GTG, in the correct reading frameupstream of the nucleic acid sequence.

A wide variety of host/expression vector combinations may be employed inexpressing the nucleic acid sequences of this invention. Usefulexpression vectors, for example, may consist of segments of chromosomal,non-chromosomal and synthetic nucleic acid sequences.

In one embodiment, prokaryotic cells may be used with an appropriatevector. Prokaryotic host cells are often used for cloning andexpression. In a preferred embodiment, prokaryotic host cells include E.coli, Pseudomonas, Bacillus and Streptomyces. In a preferred embodiment,bacterial host cells are used to express the nucleic acid molecules ofthe instant invention. Useful expression vectors for bacterial hostsinclude bacterial plasmids, such as those from E. coli, Bacillus orStreptomyces, including pBluescript, pGEX-2T, pUC vectors, col E1, pCR1,pBR322, pMB9 and their derivatives, wider host range plasmids, such asRP4, phage DNAs, e.g., the numerous derivatives of phage lambda, e.g.,NM989, λGT10 and λGT11, and other phages, e.g., M13 and filamentoussingle-stranded phage DNA. Where E. coli is used as host, selectablemarkers are, analogously, chosen for selectivity in gram negativebacteria: e.g., typical markers confer resistance to antibiotics, suchas ampicillin, tetracycline, chloramphenicol, kanamycin, streptomycinand zeocin; auxotrophic markers can also be used.

In other embodiments, eukaryotic host cells, such as yeast, insect,mammalian or plant cells, may be used. Yeast cells, typically S.cerevisiae, are useful for eukaryotic genetic studies, due to the easeof targeting genetic changes by homologous recombination and the abilityto easily complement genetic defects using recombinantly expressedproteins. Yeast cells are useful for identifying interacting proteincomponents, e.g. through use of a two-hybrid system. In a preferredembodiment, yeast cells are useful for protein expression. Vectors ofthe present invention for use in yeast will typically, but notinvariably, contain an origin of replication suitable for use in yeastand a selectable marker that is functional in yeast. Yeast vectorsinclude Yeast Integrating plasmids (e.g., YIp5) and Yeast Replicatingplasmids (the YRp and YEp series plasmids), Yeast Centromere plasmids(the YCp series plasmids), Yeast Artificial Chromosomes (YACs) which arebased on yeast linear plasmids, denoted YLp, pGPD-2, 2μ plasmids andderivatives thereof, and improved shuttle vectors such as thosedescribed in Gietz et al., Gene, 74:

527-34 (1988) (YIplac, YEplac and YCplac). Selectable markers in yeastvectors include a variety of auxotrophic markers, the most common ofwhich are (in Saccharomyces cerevisiae) URA3, HIS3, LEU2, TRP1 and LYS2,which complement specific auxotrophic mutations, such as ura3-52,his3-D1, leu2-D1, trp1-D1 and lys2-201.

Insect cells may be chosen for high efficiency protein expression. Wherethe host cells are from Spodoptera frugiperda, e.g., Sf9 and Sf21 celllines, and expresSF™ cells (Protein Sciences Corp., Meriden, Conn.,USA), the vector replicative strategy is typically based upon thebaculovirus life cycle. Typically, baculovirus transfer vectors are usedto replace the wild-type AcMNPV polyhedrin gene with a heterologous geneof interest. Sequences that flank the polyhedrin gene in the wild-typegenome are positioned 5′ and 3′ of the expression cassette on thetransfer vectors. Following co-transfection with AcMNPV DNA, ahomologous recombination event occurs between these sequences resultingin a recombinant virus carrying the gene of interest and the polyhedrinor p10 promoter. Selection can be based upon visual screening for lacZfusion activity.

The host cells may also be mammalian cells, which are particularlyuseful for expression of proteins intended as pharmaceutical agents, andfor screening of potential agonists and antagonists of a protein or aphysiological pathway. Mammalian vectors intended for autonomousextrachromosomal replication will typically include a viral origin, suchas the SV40 origin (for replication in cell lines expressing the largeT-antigen, such as COS1 and COS7 cells), the papillomavirus origin, orthe EBV origin for long term episomal replication (for use, e.g., in293-EBNA cells, which constitutively express the EBV EBNA-1 gene productand adenovirus E1A). Vectors intended for integration, and thusreplication as part of the mammalian chromosome, can, but need not,include an origin of replication functional in mammalian cells, such asthe SV40 origin. Vectors based upon viruses, such as adenovirus,adeno-associated virus, vaccinia virus, and various mammalianretroviruses, will typically replicate according to the viralreplicative strategy. Selectable markers for use in mammalian cellsinclude, but are not limited to, resistance to neomycin (G418),blasticidin, hygromycin and zeocin, and selection based upon the purinesalvage pathway using HAT medium.

Expression in mammalian cells can be achieved using a variety ofplasmids, including pSV2, pBC12BI, and p91023, as well as lytic virusvectors (e.g. vaccinia virus, adeno virus, and baculovirus), episomalvirus vectors (e.g., bovine papillomavirus), and retroviral vectors(e.g., murine retroviruses). Useful vectors for insect cells includebaculoviral vectors and pVL 941.

Plant cells can also be used for expression, with the vector replicontypically derived from a plant virus (e.g., cauliflower mosaic virus,CaMV; tobacco mosaic virus, TMV) and selectable markers chosen forsuitability in plants.

It is known that codon usage of different host cells may be differentFor example, a plant cell and a human cell may exhibit a difference incodon preference for encoding a particular amino acid. As a result,human mRNA may not be efficiently translated in a plant, bacteria orinsect host cell. Therefore, another embodiment of this invention isdirected to codon optimization. The codons of the nucleic acid moleculesof the invention may be modified to resemble, as much as possible, genesnaturally contained within the host cell without altering the amino acidsequence encoded by the nucleic acid molecule.

Any of a wide variety of expression control sequences may be used inthese vectors to express the nucleic acid molecules of this invention.Such useful expression control sequences include the expression controlsequences associated with structural genes of the foregoing expressionvectors. Expression control sequences that control transcriptioninclude, e.g., promoters, enhancers and transcription termination sites.Expression control sequences in eukaryotic cells that controlpost-transcriptional events include splice donor and acceptor sites andsequences that modify the half-life of the transcribed RNA, e.g.,sequences that direct poly(A) addition or binding sites for RNA-bindingproteins. Expression control sequences that control translation includeribosome binding sites, sequences which direct targeted expression ofthe polypeptide to or within particular cellular compartments, andsequences in the 5′ and 3′ untranslated regions that modify the rate orefficiency of translation.

Examples of useful expression control sequences for a prokaryote, e.g.,E. coli, will include a promoter, often a phage promoter, such as phagelambda pL promoter, the trc promoter, a hybrid derived from the trp andlac promoters, the bacteriophage T7 promoter (in E. coli cellsengineered to express the T7 polymerase), the TAC or TRC system, themajor operator and promoter regions of phage lambda, the control regionsof fd coat protein, and the araBAD operon. Prokaryotic expressionvectors may further include transcription terminators, such as the aspAterminator, and elements that facilitate translation, such as aconsensus ribosome binding site and translation termination codon,Schomer et al., Proc. Natl. Acad. Sci. USA 83: 8506-8510 (1986).

Expression control sequences for yeast cells, typically S. cerevisiae,will include a yeast promoter, such as the CYC1 promoter, the GAL1promoter, the GAL10 promoter, ADH1 promoter, the promoters of the yeastα-mating system, or the GPD promoter, and will typically have elementsthat facilitate transcription termination, such as the transcriptiontermination signals from the CYC1 or ADH1 gene.

Expression vectors useful for expressing proteins in mammalian cellswill include a promoter active in mammalian cells. These promotersinclude, but are not limited to, those derived from mammalian viruses,such as the enhancer-promoter sequences from the immediate early gene ofthe human cytomegalovirus (CMV), the enhancer-promoter sequences fromthe Rous sarcoma virus long terminal repeat (RSV LTR), theenhancer-promoter from SV40 and the early and late promoters ofadenovirus. Other expression control sequences include the promoter for3-phosphoglycerate kinase or other glycolytic enzymes, the promoters ofacid phosphatase. Other expression control sequences include those fromthe gene comprising the OSNA of interest. Often, expression is enhancedby incorporation of polyadenylation sites, such as the late SV40polyadenylation site and the polyadenylation signal and transcriptiontermination sequences from the bovine growth hormone (BGH) gene, andribosome binding sites. Furthermore, vectors can include introns, suchas intron II of rabbit β-globin gene and the SV40 splice elements.

Preferred nucleic acid vectors also include a selectable or amplifiablemarker gene and means for amplifying the copy number of the gene ofinterest. Such marker genes are well known in the art. Nucleic acidvectors may also comprise stabilizing sequences (e.g., ori- or ARS-likesequences and telomere-like sequences), or may alternatively be designedto favor directed or non-directed integration into the host cell genome.In a preferred embodiment, nucleic acid sequences of this invention areinserted in frame into an expression vector that allows a high levelexpression of an RNA which encodes a protein comprising the encodednucleic acid sequence of interest. Nucleic acid cloning and sequencingmethods are well known to those of skill in the art and are described inan assortment of laboratory manuals, including Sambrook (1989), supra,Sambrook (2000), supra; Ausubel (1992), supra; and Ausubel (1999),supra. Product information from manufacturers of biological, chemicaland immunological reagents also provide useful information.

Expression vectors may be either constitutive or inducible. Induciblevectors include either naturally inducible promoters, such as the trcpromoter, which is regulated by the lac operon, and the pL promoter,which is regulated by tryptophan, the MMTV-LTR promoter, which isinducible by dexamethasone, or can contain synthetic promoters and/oradditional elements that confer inducible control on adjacent promoters.Examples of inducible synthetic promoters are the hybrid Plac/ara-1promoter and the PLtetO-1 promoter. The PLtetO-1 promoter takesadvantage of the high expression levels from the PL promoter of phagelambda, but replaces the lambda repressor sites with two copies ofoperator 2 of the Tn10 tetracycline resistance operon, causing thispromoter to be tightly repressed by the Tet repressor protein andinduced in response to tetracycline (Tc) and Tc derivatives such asanhydrotetracycline. Vectors may also be inducible because they containhormone response elements, such as the glucocorticoid response element(GRE) and the estrogen response element (ERE), which can confer hormoneinducibility where vectors are used for expression in cells having therespective hormone receptors. To reduce background levels of expression,elements responsive to ecdysone, an insect hormone, can be used instead,with coexpression of the ecdysone receptor.

In one embodiment of the invention, expression vectors can be designedto fuse the expressed polypeptide to small protein tags that facilitatepurification and/or visualization. Such tags include a polyhistidine tagthat facilitates purification of the fusion protein by immobilized metalaffinity chromatography, for example using NiNTA resin (Qiagen Inc.,Valencia, Calif., USA) or TALON™ resin (cobalt immobilized affinitychromatography medium, Clontech Labs, Palo Alto, Calif., USA). Thefusion protein can include a chitin-binding tag and self-excisingintein, permitting chitin-based purification with self-removal of thefused tag (IMPACT™ system, New England Biolabs, Inc., Beverley, Mass.,USA). Alternatively, the fusion protein can include a calmodulin-bindingpeptide tag, permitting purification by calmodulin affinity resin(Stratagene, La Jolla, Calif., USA), or a specifically excisablefragment of the biotin carboxylase carrier protein, permittingpurification of in vivo biotinylated protein using an avidin resin andsubsequent tag removal (Promega, Madison, Wisc., USA). As another usefulalternative, the polypeptides of the present invention can be expressedas a fusion to glutathione-S-transferase, the affinity and specificityof binding to glutathione permitting purification using glutathioneaffinity resins, such as Glutathione-Superflow Resin (ClontechLaboratories, Palo Alto, Calif., USA), with subsequent elution with freeglutathione. Other tags include, for example, the Xpress epitope,detectable by anti-Xpress antibody (Invitrogen, Carlsbad, Calif., USA),a myc tag, detectable by anti-myc tag antibody, the V5 epitope,detectable by anti-V5 antibody (Invitrogen, Carlsbad, Calif., USA),FLAG® epitope, detectable by anti-FLAG® antibody (Stratagene, La Jolla,Calif., USA), and the HA epitope, detectable by anti-HA antibody.

For secretion of expressed polypeptides, vectors can include appropriatesequences that encode secretion signals, such as leader peptides. Forexample, the pSecTag2 vectors (Invitrogen, Carlsbad, Calif., USA) are5.2 kb mammalian expression vectors that carry the secretion signal fromthe V-J2-C region of the mouse Ig kappa-chain for efficient secretion ofrecombinant proteins from a variety of mammalian cell lines.

Expression vectors can also be designed to fuse proteins encoded by theheterologous nucleic acid insert to polypeptides that are larger thanpurification and/or identification tags. Useful protein fusions includethose that permit display of the encoded protein on the surface of aphage or cell, fusions to intrinsically fluorescent proteins, such asthose that have a green fluorescent protein (GFP)-like chromophore,fusions to the IgG Fc region, and fusions for use in two hybrid systems.

Vectors for phage display fuse the encoded polypeptide to, e.g., thegene III protein (pIII) or gene VIII protein (pVII) for display on thesurface of filamentous phage, such as M13. See Barbas et al., PhageDisplay: A Laboratory Manual, Cold Spring Harbor Laboratory Press(2001); Kay et al. (eds.), Phage Display of Peptides and Proteins: ALaboratory Manual, Academic Press, Inc., (1996); Abelson et al. (eds.),Combinatorial Chemistry (Methods in Enzymology, Vol. 267) Academic Press(1996). Vectors for yeast display, e.g. the pYD1 yeast display vector(Invitrogen, Carlsbad, Calif., USA), use the α-agglutinin yeast adhesionreceptor to display recombinant protein on the surface of S. cerevisiae.Vectors for mammalian display, e.g., the pDisplay™ vector (Invitrogen,Carlsbad, Calif., USA), target recombinant proteins using an N-terminalcell surface targeting signal and a C-terminal transmembrane anchoringdomain of platelet derived growth factor receptor.

A wide variety of vectors now exist that fuse proteins encoded byheterologous nucleic acids to the chromophore of thesubstrate-independent, intrinsically fluorescent green fluorescentprotein from Aequorea victoria (“GFP”) and its variants. The GFP-likechromophore can be selected from GFP-like chromophores found innaturally occurring proteins, such as A. victoria GFP (GenBank accessionnumber AAA27721), Renilla reniformis GFP, FP583 (GenBank accession no.AF168419) (DsRed), FP593 (AF272711), FP483 (AF168420), FP484 (AF168424),FP595 (AF246709), FP486 (AF168421), FP538 (AF168423), and FP506(AF168422), and need include only so much of the native protein as isneeded to retain the chromophore's intrinsic fluorescence. Methods fordetermining the minimal domain required for fluorescence are known inthe art. See Li et al., J. Biol. Chem. 272: 28545-28549 (1997).Alternatively, the GFP-like chromophore can be selected from GFP-likechromophores modified from those found in nature. The methods forengineering such modified GFP-like chromophores and testing them forfluorescence activity, both alone and as part of protein fusions, arewell known in the art. See Heim et al., Curr. Biol 6: 178-182 (1996) andPalm et al., Methods Enzymol. 302: 378-394 (1999). A variety of suchmodified chromophores are now commercially available and can readily beused in the fusion proteins of the present invention. These include EGFP(“enhanced GFP”), EBFP (“enhanced blue fluorescent protein”), BFP2, EYFP(“enhanced yellow fluorescent protein”), ECFP (“enhanced cyanfluorescent protein”) or Citrine. EGFP (see, e.g. Cormack et al., Gene173: 33-38 (1996); U.S. Pat. Nos. 6,090,919 and 5,804,387, thedisclosures of which are incorporated herein by reference in theirentireties) is found on a variety of vectors, both plasmid and viral,which are available commercially (Clontech Labs, Palo Alto, Calif.,USA); EBFP is optimized for expression in mammalian cells whereas BFP2,which retains the original jellyfish codons, can be expressed inbacteria (see, e.g., Heim et al., Curr. Biol. 6: 178-182 (1996) andCormack et al., Gene 173: 33-38 (1996)). Vectors containing theseblue-shifted variants are available from Clontech Labs (Palo Alto,Calif., USA). Vectors containing EYFP, ECFP (see, e.g. Heim et al.,Curr. Biol. 6: 178-182 (1996); Miyawaki et al., Nature 388: 882-887(1997)) and Citrine (see, e.g., Heikal et al., Proc. Natl. Acad. Sci.USA 97: 11996-12001 (2000)) are also available from Clontech Labs. TheGFP-like chromophore can also be drawn from other modified GFPs,including those described in U.S. Pat. Nos. 6,124,128; 6,096,865;6,090,919; 6,066,476; 6,054,321; 6,027,881; 5,968,750; 5,874,304;5,804,387; 5,777,079; 5,741,668; and 5,625,048, the disclosures of whichare incorporated herein by reference in their entireties. See also Conn(ed.), Green Fluorescent Protein (Methods in Enzymology, Vol. 302),Academic Press, Inc. (1999); Yang, et al., J Biol Chem, 273: 8212-6(1998); Bevis et al., Nature Biotechnology, 20:83-7 (2002). The GFP-likechromophore of each of these GFP variants can usefully be included inthe fusion proteins of the present invention.

Fusions to the IgG Fc region increase serum half-life of proteinpharmaceutical products through interaction with the FcRn receptor (alsodenominated the FcRp receptor and the Brambell receptor, FcRb), furtherdescribed in International Patent Application Nos. WO 97/43316, WO97/34631, WO 96/32478, and WO 96/18412, the disclosures of which areincorporated herein by reference in their entireties.

For long-term, high-yield recombinant production of the polypeptides ofthe present invention, stable expression is preferred. Stable expressionis readily achieved by integration into the host cell genome of vectorshaving selectable markers, followed by selection of these integrants.Vectors such as pUB6/V5-His A, B, and C (Invitrogen, Carlsbad, Calif.,USA) are designed for high-level stable expression of heterologousproteins in a wide range of mammalian tissue types and cell lines.pUB6/V5-His uses the promoter/enhancer sequence from the human ubiquitinC gene to drive expression of recombinant proteins: expression levels in293, CHO, and NIH3T3 cells are comparable to levels from the CMV andhuman EF-1a promoters. The bsd gene permits rapid selection of stablytransfected mammalian cells with the potent antibiotic blasticidin.

Replication incompetent retroviral vectors, typically derived fromMoloney murine leukemia virus, also are useful for creating stabletransfectants having integrated provirus. The highly efficienttransduction machinery of retroviruses, coupled with the availability ofa variety of packaging cell lines such as RetroPack™ PT 67,EcoPack2™-293, AmphoPack-293, and GP2-293 cell lines (all available fromClontech Laboratories, Palo Alto, Calif., USA) allow a wide host rangeto be infected with high efficiency; varying the multiplicity ofinfection readily adjusts the copy number of the integrated provirus.

Of course, not all vectors and expression control sequences willfunction equally well to express the nucleic acid molecules of thisinvention. Neither will all hosts function equally well with the sameexpression system. However, one of skill in the art may make a selectionamong these vectors, expression control sequences and hosts withoutundue experimentation and without departing from the scope of thisinvention. For example, in selecting a vector, the host must beconsidered because the vector must be replicated in it. The vector'scopy number, the ability to control that copy number, the ability tocontrol integration, if any, and the expression of any other proteinsencoded by the vector, such as an antibiotic or other selection marker,should also be considered. The present invention further includes hostcells comprising the vectors of the present invention, either presentepisomally within the cell or integrated, in whole or in part, into thehost cell chromosome. Among other considerations, some of which aredescribed above, a host cell strain may be chosen for its ability toprocess the expressed polypeptide in the desired fashion. Suchpost-translational modifications of the polypeptide include, but are notlimited to, acetylation, carboxylation, glycosylation, phosphorylation,lipidation, and acylation, and it is an aspect of the present inventionto provide OSPs with such post-translational modifications.

In selecting an expression control sequence, a variety of factors shouldalso be considered. These include, for example, the relative strength ofthe sequence, its controllability, and its compatibility with thenucleic acid molecules of this invention, particularly with regard topotential secondary structures. Unicellular hosts should be selected byconsideration of their compatibility with the chosen vector, thetoxicity of the product coded for by the nucleic acid sequences of thisinvention, their secretion characteristics, their ability to fold thepolypeptide correctly, their fermentation or culture requirements, andthe ease of purification from them of the products coded for by thenucleic acid molecules of this invention.

The recombinant nucleic acid molecules and more particularly, theexpression vectors of this invention may be used to express thepolypeptides of this invention as recombinant polypeptides in aheterologous host cell. The polypeptides of this invention may befull-length or less than full-length polypeptide fragments recombinantlyexpressed from the nucleic acid molecules according to this invention.Such polypeptides include analogs, derivatives and muteins that may ormay not have biological activity.

Vectors of the present invention will also often include elements thatpermit in vitro transcription of RNA from the inserted heterologousnucleic acid. Such vectors typically include a phage promoter, such asthat from T7, T3, or SP6, flanking the nucleic acid insert. Often twodifferent such promoters flank the inserted nucleic acid, permittingseparate in vitro production of both sense and antisense strands.

Transformation and other methods of introducing nucleic acids into ahost cell (e.g., conjugation, protoplast transformation or fusion,transfection, electroporation, liposome delivery, membrane fusiontechniques, high velocity DNA-coated pellets, viral infection andprotoplast fusion) can be accomplished by a variety of methods which arewell known in the art (See, for instance, Ausubel, supra, and Sambrooket al., supra). Bacterial, yeast, plant or mammalian cells aretransformed or transfected with an expression vector, such as a plasmid,a cosmid, or the like, wherein the expression vector comprises thenucleic acid of interest. Alternatively, the cells may be infected by aviral expression vector comprising the nucleic acid of interest.Depending upon the host cell, vector, and method of transformation used,transient or stable expression of the polypeptide will be constitutiveor inducible. One having ordinary skill in the art will be able todecide whether to express a polypeptide transiently or stably, andwhether to express the protein constitutively or inducibly.

A wide variety of unicellular host cells are useful in expressing theDNA sequences of this invention. These hosts may include well knowneukaryotic and prokaryotic hosts, such as strains of, fungi, yeast,insect cells such as Spodoptera frugiperda (SF9), animal cells such asCHO, as well as plant cells in tissue culture. Representative examplesof appropriate host cells include, but are not limited to, bacterialcells, such as E. coli, Caulobacter crescentus, Streptomyces species,and Salmonella typhimurium; yeast cells, such as Saccharomycescerevisiae, Schizosaccharomyces pombe, Pichia pastoris, Pichiamethanolica; insect cell lines, such as those from Spodopterafrugiperda, e.g., Sf9 and Sf21 cell lines, and expresSF™ cells (ProteinSciences Corp., Meriden, Conn., USA), Drosophila S2 cells, andTrichoplusia ni High Five® Cells (Invitrogen, Carlsbad, Calif., USA);and mammalian cells. Typical mammalian cells include BHK cells, BSC 1cells, BSC 40 cells, BMT 10 cells, VERO cells, COS1 cells, COS7 cells,Chinese hamster ovary (CHO) cells, 3T3 cells, NIH 3T3 cells, 293 cells,HEPG2 cells, HeLa cells, L cells, MDCK cells, HEK293 cells, WI38 cells,murine ES cell lines (e.g., from strains 129/SV, C57/BL6, DBA-1,129/SVJ), K562 cells, Jurkat cells, and BW5147 cells. Other mammaliancell lines are well known and readily available from the American TypeCulture Collection (ATCC) (Manassas, Va., USA) and the NationalInstitute of General Medical Sciences (NIGMS) Human Genetic CellRepository at the Coriell Cell Repositories (Camden, N.J., USA). Cellsor cell lines derived from ovarian are particularly preferred becausethey may provide a more native post-translational processing.Particularly preferred are human ovarian cells.

Particular details of the transfection, expression and purification ofrecombinant proteins are well documented and are understood by those ofskill in the art. Further details on the various technical aspects ofeach of the steps used in recombinant production of foreign genes inbacterial cell expression systems can be found in a number of texts andlaboratory manuals in the art. See, e.g., Ausubel (1992), supra, Ausubel(1999), supra, Sambrook (1989), supra, and Sambrook (2001), supra.

Methods for introducing the vectors and nucleic acid molecules of thepresent invention into the host cells are well known in the art; thechoice of technique will depend primarily upon the specific vector to beintroduced and the host cell chosen.

Nucleic acid molecules and vectors may be introduced into prokaryotes,such as E. coli, in a number of ways. For instance, phage lambda vectorswill typically be packaged using a packaging extract (e.g., Gigapack®packaging extract, Stratagene, La Jolla, Calif., USA), and the packagedvirus used to infect E. coli.

Plasmid vectors will typically be introduced into chemically competentor electrocompetent bacterial cells. E. coli cells can be renderedchemically competent by treatment, e.g., with CaCl₂, or a solution ofMg²⁺, Mn²⁺, Ca²⁺, Rb⁺ or K⁺, dimethyl sulfoxide, dithiothreitol, andhexamine cobalt (III), Hanahan, J. Mol. Biol. 166(4):557-80 (1983), andvectors introduced by heat shocks A wide variety of chemically competentstrains are also available commercially (e.g., Epicurian Coli®XL10-Gold® Ultracompetent Cells (Stratagene, La Jolla, Calif., USA);DH5α competent cells (Clontech Laboratories, Palo Alto, Calif., USA);and TOP10 Chemically Competent E. coli Kit (Invitrogen, Carlsbad,Calif., USA)). Bacterial cells can be rendered electrocompetent to takeup exogenous DNA by electroporation by various pre-pulse treatments;vectors are introduced by electroporation followed by subsequentoutgrowth in selected media. An extensive series of protocols isprovided by BioRad (Richmond, Calif., USA).

Vectors can be introduced into yeast cells by spheroplasting, treatmentwith lithium salts, electroporation, or protoplast fusion. Spheroplastsare prepared by the action of hydrolytic enzymes such as a snail-gutextract, usually denoted Glusulase or Zymolyase, or an enzyme fromArthrobacter luteus to remove portions of the cell wall in the presenceof osmotic stabilizers, typically 1 M sorbitol. DNA is added to thespheroplasts, and the mixture is co-precipitated with a solution ofpolyethylene glycol (PEG) and Ca²⁺. Subsequently, the cells areresuspended in a solution of sorbitol, mixed with molten agar and thenlayered on the surface of a selective plate containing sorbitol.

For lithium-mediated transformation, yeast cells are treated withlithium acetate to permeabilize the cell wall, DNA is added and thecells are co-precipitated with PEG. The cells are exposed to a briefheat shock, washed free of PEG and lithium acetate, and subsequentlyspread on plates containing ordinary selective medium. Increasedfrequencies of transformation are obtained by using specially-preparedsingle-stranded carrier DNA and certain organic solvents. Schiestl etal., Curr. Genet. 16(5-6): 339-46 (1989).

For electroporation, freshly-grown yeast cultures are typically washed,suspended in an osmotic protectant, such as sorbitol, mixed with DNA,and the cell suspension pulsed in an electroporation device.Subsequently, the cells are spread on the surface of plates containingselective media. Becker et al., Methods Enzymol. 194: 182-187 (1991).The efficiency of transformation by electroporation can be increasedover 100-fold by using PEG, single-stranded carrier DNA and cells thatare in late log-phase of growth. Larger constructs, such as YACs, can beintroduced by protoplast fusion.

Mammalian and insect cells can be directly infected by packaged viralvectors, or transfected by chemical or electrical means. For chemicaltransfection, DNA can be coprecipitated with CaPO₄ or introduced usingliposomal and nonliposomal lipid-based agents. Commercial kits areavailable for CaPO₄ transfection (CalPhos™ Mammalian Transfection Kit,Clontech Laboratories, Palo Alto, Calif., USA), and lipid-mediatedtransfection can be practiced using commercial reagents, such asLIPOFECTAMINE™ 2000, LIPOFECTAMINE™ Reagent, CELLFECTIN® Reagent, andLIPOFECTIN® Reagent Invitrogen, Carlsbad, Calif., USA), DOTAP LiposomalTransfection Reagent, FuGENE 6, X-tremeGENE Q2, DOSPER, (Roche MolecularBiochemicals, Indianapolis, Ind. USA), Effectene™, PolyFect®, Superfect®(Qiagen, Inc., Valencia, Calif., USA). Protocols for electroporatingmammalian cells can be found in, for example; Norton et al. (eds.), GeneTransfer Methods: Introducing DNA into Living Cells and Organisms,BioTechniques Books, Eaton Publishing Co. (2000). Other transfectiontechniques include transfection by particle bombardment andmicroinjection. See, e.g. Cheng et al., Proc. Natl. Acad. Sci. USA90(10): 4455-9 (1993); Yang et al., Proc. Natl. Acad. Sci. USA 87(24):9568-72 (1990).

Production of the recombinantly produced proteins of the presentinvention can optionally be followed by purification.

Purification of recombinantly expressed proteins is now well within theskill in the art and thus need not be detailed here. See, e.g., Thorneret al. (eds.), Applications of Chimeric Genes and Hybrid Proteins, PartA: Gene Expression and Protein Purification (Methods in Enzymology, Vol.326), Academic Press (2000); Harbin (ed.), Cloning, Gene Expression andProtein Purification: Experimental Procedures and Process Rationale,Oxford Univ. Press (2001); Marshak et al., Strategies for ProteinPurification and Characterization: A Laboratory Course Manual, ColdSpring Harbor Laboratory Press (1996); and Roe (ed.), ProteinPurification Applications, Oxford University Press (2001).

Briefly, however, if purification tags have been fused through use of anexpression vector that appends such tags, purification can be effected,at least in part, by means appropriate to the tag, such as use ofimmobilized metal affinity chromatography for polyhistidine tags. Othertechniques common in the art include ammonium sulfate fractionation,immunoprecipitation, fast protein liquid chromatography (FPLC), highperformance liquid chromatography (HPLC), and preparative gelelectrophoresis.

Polypeptides including Fragments Muteins, Homologous Proteins, AllelicVariants, Analogs and Derivatives

Another aspect of the invention relates to polypeptides encoded by thenucleic acid molecules described herein. In a preferred embodiment, thepolypeptide is an ovarian specific polypeptide (OSP). In an even morepreferred embodiment, the polypeptide comprises an amino acid sequenceof SEQ ED NO: 129-295 or is derived from a polypeptide having the aminoacid sequence of SEQ ID NO: 129-295. A polypeptide as defined herein maybe produced recombinantly, as discussed supra, may be isolated from acell that naturally expresses the protein, or may be chemicallysynthesized following the teachings of the specification and usingmethods well known to those having ordinary skill in the art.

Polypeptides of the present invention may also comprise a part orfragment of an OSP. In a preferred embodiment, the fragment is derivedfrom a polypeptide having an amino acid sequence selected from the groupconsisting of SEQ ED NO: 129-295. Polypeptides of the present inventioncomprising a part or fragment of an entire OSP may or may not be OSPs.For example, a full-length polypeptide may be ovarian-specific, while afragment thereof may be found in other tissues as well as in ovarian. Apolypeptide that is not an OSP, whether it is a fragment, analog,mutein, homologous protein or derivative, is nevertheless useful,especially for immunizing animals to prepare anti-OSP antibodies. In apreferred embodiment, the part or fragment is an OSP. Methods ofdetermining whether a polypeptide of the present invention is an OSP aredescribed infra.

Polypeptides of the present invention comprising fragments of at least 6contiguous amino acids are also useful in mapping B cell and T cellepitopes of the reference protein. See, e.g., Geysen et al., Proc. Natl.Acad. Sci. USA 81: 3998-4002 (1984) and U.S. Pat. Nos. 4,708,871 and5,595,915, the disclosures of which are incorporated herein by referencein their entireties. Because the fragment need not itself beimmunogenic, part of an immunodominant epitope, nor even recognized bynative antibody, to be useful in such epitope mapping, all fragments ofat least 6 amino acids of a polypeptide of the present invention haveutility in such a study.

Polypeptides of the present invention comprising fragments of at least 8contiguous amino acids, often at least 15 contiguous amino acids, areuseful as immunogens for raising antibodies that recognize polypeptidesof the present invention. See, e.g., Lemer, Nature 299: 592-596 (1982);Shinnick et al., Annu. Rev. Microbiol. 37: 425-46 (1983); Sutcliffe etal., Science 219: 660-6 (1983). As further described in the above-citedreferences, virtually all 8-mers, conjugated to a carrier, such as aprotein, prove immunogenic and are capable of eliciting antibody for theconjugated peptide; accordingly, all fragments of at least 8 amino acidsof the polypeptides of the present invention have utility as immunogens.

Polypeptides comprising fragments of at least 8, 9, 10 or 12 contiguousamino acids are also useful as competitive inhibitors of binding of theentire polypeptide, or a portion thereof, to antibodies (as in epitopemapping), and to natural binding partners, such as subunits in amultimeric complex or to receptors or ligands of the subject protein;this competitive inhibition permits identification and separation ofmolecules that bind specifically to the polypeptide of interest. SeeU.S. Pat. Nos. 5,539,084 and 5,783,674, incorporated herein by referencein their entireties.

The polypeptide of the present invention thus preferably is at least 6amino acids in length, typically at least 8, 9, 10 or 12 amino acids inlength, and often at least 15 amino acids in length. Often, thepolypeptide of the present invention is at least 20 amino acids inlength, even 25 amino acids, 30 amino acids, 35 amino acids, or 50 aminoacids or more in length. Of course, larger polypeptides having at least75 amino acids, 100 amino acids, or even 150 amino acids are alsouseful, and at times preferred.

One having ordinary skill in the art can produce fragments by truncatingthe nucleic acid molecule, e.g., an OSNA, encoding the polypeptide andthen expressing it recombinantly. Alternatively, one can produce afragment by chemically synthesizing a portion of the full-lengthpolypeptide. One may also produce a fragment by enzymatically cleavingeither a recombinant polypeptide or an isolated naturally occurringpolypeptide. Methods of producing polypeptide fragments are well knownin the art. See, e.g., Sambrook (1989), supra; Sambrook (2001), supra;Ausubel (1992), supra; and Ausubel (1999), supra. In one embodiment, apolypeptide comprising only a fragment, preferably a fragment of an OSP,may be produced by chemical or enzymatic cleavage of an OSP polypeptide.In a preferred embodiment, a polypeptide fragment is produced byexpressing a nucleic acid molecule of the present invention encoding afragment, preferably of an OSP, in a host cell.

Polypeptides of the present invention are also inclusive of mutants,fusion proteins, homologous proteins and allelic variants.

A mutant protein, or mutein, may have the same or different propertiescompared to a naturally occurring polypeptide and comprises at least oneamino acid insertion, duplication, deletion, rearrangement orsubstitution compared to the amino acid sequence of a nativepolypeptide. Small deletions and insertions can often be found that donot alter the function of a protein. Muteins may or may not beovarian-specific. Preferably, the mutein is ovarian-specific. Morepreferably the mutein is a polypeptide that comprises at least one aminoacid insertion, duplication, deletion, rearrangement or substitutioncompared to the amino acid sequence of SEQ ID NO: 129-295. Accordingly,in a preferred embodiment, the mutein is one that exhibits at least 50%sequence identity, more preferably at least 60%. sequence identity, evenmore preferably at least 70%, yet more preferably at least 80% sequenceidentity to an OSP comprising an amino acid sequence of SEQ ID NO:129-295. In a yet more preferred embodiment, the mutein exhibits atleast 85%, more preferably 90%, even more preferably 95% or 96%, and yetmore preferably at least 97%, 98%, 99% or 99.5% sequence identity to anOSP comprising an amino acid sequence of SEQ ID NO: 129-295.

A mutein may be produced by isolation from a naturally occurring mutantcell, tissue or organism. A mutein may be produced by isolation from acell, tissue or organism that has been experimentally mutagenized.Alternatively, a mutein may be produced by chemical manipulation of apolypeptide, such as by altering the amino acid residue to another aminoacid residue using synthetic or semi-synthetic chemical techniques. In apreferred embodiment, a mutein is produced from a host cell comprising amutated nucleic acid molecule compared to the naturally occurringnucleic acid molecule. For instance, one may produce a mutein of apolypeptide by introducing one or more mutations into a nucleic acidmolecule of the invention and then expressing it recombinantly. Thesemutations may be targeted, in which particular encoded amino acids arealtered, or may be untargeted, in which random encoded amino acidswithin the polypeptide are altered. Muteins with random amino acidalterations can be screened for a particular biological activity orproperty, particularly whether the polypeptide is ovarian-specific, asdescribed below. Multiple random mutations can be introduced into thegene by methods well known to the art, e.g., by error-prone PCR,shuffling, oligonucleotide-directed mutagenesis, assembly PCR, sexualPCR mutagenesis, in vivo mutagenesis, cassette mutagenesis, recursiveensemble mutagenesis, exponential ensemble mutagenesis and site-specificmutagenesis. Methods of producing muteins with targeted or random aminoacid alterations are well known in the art. See, e.g., Sambrook (1989),supra; Sambrook (2001), supra; Ausubel (1992), supra; and Ausubel(1999), as well as U.S. Pat. No. 5,223,408, which is herein incorporatedby reference in its entirety.

The invention also contemplates polypeptides that are homologous to apolypeptide of the invention. In a preferred embodiment, the polypeptideis homologous to an OSP. In an even more preferred embodiment, thepolypeptide is homologous to an OSP selected from the group having anamino acid sequence of SEQ ID NO: 129-295. By homologous polypeptide itis meant one that exhibits significant sequence identity to an OSP,preferably an OSP having an amino acid sequence of SEQ ID NO: 129-295.By significant sequence identity it is meant that the homologouspolypeptide exhibits at least 50% sequence identity, more preferably atleast 60% sequence identity, even more preferably at least 70%, yet morepreferably at least 80% sequence identity to an OSP comprising an aminoacid sequence of SEQ ID NO: 129-295. More preferred are homologouspolypeptides exhibiting at least 85%, more preferably 90%, even morepreferably 95% or 96%, and yet more preferably at least 97% or 98%sequence identity to an OSP comprising an amino acid sequence of SEQ IDNO: 129-295. Most preferably, the homologous polypeptide exhibits atleast 99%, more preferably 99.5%, even more preferably 99.6%, 99.7%,99.8% or 99.9% sequence identity to an OSP comprising an amino acidsequence of SEQ ID NO: 129-295. In a preferred embodiment, the aminoacid substitutions of the homologous polypeptide are conservative aminoacid substitutions as discussed supra.

Homologous polypeptides of the present invention also comprisepolypeptide encoded by a nucleic acid molecule that selectivelyhybridizes to an OSNA or an antisense sequence thereof. In thisembodiment, it is preferred that the homologous polypeptide be encodedby a nucleic acid molecule that hybridizes to an OSNA under lowstringency, moderate stringency or high stringency conditions, asdefined herein. More preferred is a homologous polypeptide encoded by anucleic acid sequence which hybridizes to a OSNA selected from the groupconsisting of SEQ ID NO: 1-128 or a homologous polypeptide encoded by anucleic acid molecule that hybridizes to a nucleic acid molecule thatencodes an OSP, preferably an OSP of SEQ ID NO:129-295 under lowstringency, moderate stringency or high stringency conditions, asdefined herein.

Homologous polypeptides of the present invention may be naturallyoccurring and derived from another species, especially one derived fromanother primate, such as chimpanzee, gorilla, rhesus macaque, or baboon,wherein the homologous polypeptide comprises an amino acid sequence thatexhibits significant sequence identity to that of SEQ ID NO: 129-295.The homologous polypeptide may also be a naturally occurring polypeptidefrom a human, when the OSP is a member of a family of polypeptides. Thehomologous polypeptide may also be a naturally occurring polypeptidederived from a non-primate, mammalian species, including withoutlimitation, domesticated species, e.g., dog, cat, mouse, rat, rabbit,guinea pig, hamster, cow, horse, goat or pig. The homologous polypeptidemay also be a naturally occurring polypeptide derived from anon-mammalian species, such as birds or reptiles. The naturallyoccurring homologous protein may be isolated directly from humans orother species. Alternatively, the nucleic acid molecule encoding thenaturally occurring homologous polypeptide may be isolated and used toexpress the homologous polypeptide recombinantly. The homologouspolypeptide may also be one that is experimentally produced by randommutation of a nucleic acid molecule and subsequent expression of thenucleic acid molecule. Alternatively, the homologous polypeptide may beone that is experimentally produced by directed mutation of one or morecodons to alter the encoded amino acid of an OSP. In a preferredembodiment, the homologous polypeptide encodes a polypeptide that is anOSP.

Relatedness of proteins can also be characterized using a secondfunctional test, such as the ability of a first protein competitively toinhibit the binding of a second protein to an antibody. It is,therefore, another aspect of the present invention to provide isolatedpolypeptides not only identical in sequence to those described withparticularity herein, but also to provide isolated polypeptides(“cross-reactive proteins”) that competitively inhibit the binding ofantibodies to all or to a portion of the isolated polypeptides of thepresent invention. Such competitive inhibition can readily be determinedusing immunoassays well known in the art.

As discussed above, single nucleotide polymorphisms (SNPs) occurfrequently in eukaryotic genomes, and the sequence determined from oneindividual of a species may differ from other allelic forms presentwithin the population. Thus, polypeptides of the present invention arealso inclusive of those encoded by an allelic variant of a nucleic acidmolecule encoding an OSP. In this embodiment, it is preferred that thepolypeptide be encoded by an allelic variant of a gene that encodes apolypeptide having the amino acid sequence selected from the groupconsisting of SEQ ID NO: 129-295. More preferred is that the polypeptidebe encoded by an allelic variant of a gene that has the nucleic acidsequence selected from the group consisting of SEQ ID NO: 1-128.

Polypeptides of the present invention are also inclusive of derivativepolypeptides encoded by a nucleic acid molecule according to the instantinvention. In this embodiment, it is preferred that the polypeptide bean OSP. Also preferred are derivative polypeptides having an amino acidsequence selected from the group consisting of SEQ ID NO: 129-295 andwhich has been acetylated, carboxylated, phosphorylated, glycosylated,ubiquitinated or post-translationally modified in another manner. Inanother preferred embodiment, the derivative has been labeled with, e.g.radioactive isotopes such as ¹²⁵I, ³²P, ³⁵S, and ³H. In anotherpreferred embodiment, the derivative has been labeled with fluorophores,chemiluminescent agents, enzymes, and antiligands that can serve asspecific binding pair members for a labeled ligand.

Polypeptide modifications are well known to those of skill and have beendescribed in great detail in the scientific literature. Severalparticularly common modifications, glycosylation, lipid attachment,sulfation, gamma-carboxylation of glutamic acid residues, hydroxylationand ADP-ribosylation, for instance, are described in most basic texts,such as, for instance Creighton, Protein Structure and MolecularProperties, 2nd ed., W. H. Freeman and Company (1993). Many detailedreviews are available on this subject, such as, for example, thoseprovided by Wold, in Johnson (ed.), Posttranslational CovalentModification of Proteins, pgs. 1-12, Academic Press (1983); Seifter etal., Meth. Enzymol. 182: 626-646 (1990) and Rattan et al., Ann. N. YAcad. Sci. 663: 48-62 (1992).

One may determine whether a polypeptide of the invention is likely to bepost-translationally modified by analyzing the sequence of thepolypeptide to determine if there are peptide motifs indicative of sitesfor post-translational modification. There are a number of computerprograms that permit prediction of post-translational modifications.See, e.g., expasy.org (accessed Nov. 11, 2002) of the world wide web,which includes PSORT, for prediction of protein sorting signals andlocalization sites, SignalP, for prediction of signal peptide cleavagesites, MITOPROT and Predotar, for prediction of mitochondrial targetingsequences, NetOGlyc, for prediction of type O-glycosylation sites inmammalian proteins, big-PI Predictor and DGPI, for prediction ofprenylation-anchor and cleavage sites, and NetPhos, for prediction ofSer, Thr and Tyr phosphorylation sites in eukaryotic proteins. Othercomputer programs, such as those included in GCG, also may be used todetermine post-translational modification peptide motifs.

General examples of types of post-translational modifications include,but are not limited to: (Z)-dehydrobutyrine; 1-chondroitinsulfate-L-aspartic acid ester, 1′-glycosyl-L-tryptophan;1′-phospho-L-histidine; 1-thioglycine; 2′-(S-L-cysteinyl)-L-histidine;2′-[3-carboxamido(trimethylammonio)propyl]-L-histidine;2′-alpha-mannosyl-L-tryptophan; 2-methyl-L-glutamine; 2-oxobutanoicacid; 2-pyrrolidone carboxylic acid; 3′-(1′-L-histidyl)-L-tyrosine;3′-(8alpha-FAD)-L-histidine; 3′-(S-L-cysteinyl)-L-tyrosine; 3′,3″,5′-triiodo-L-thyronine; 3′-4′-phospho-L-tyrosine;3-hydroxy-L-proline; 3′-methyl-L-histidine; 3-methyl-L-lanthionine;3′-phospho-L-histidine; 4′-(L-tryptophan)-L-tryptophyl quinone; 42N-cysteinyl-glycosylphosphatidylinositolethanolamine;43-(T-L-histidyl)-L-tyrosine; 4-hydroxy-L-arginine; 4-hydroxy-L-lysine;4-hydroxy-L-proline; 5′-(N6-L-lysine)-L-topaquinone; 5-hydroxy-L-lysine;5-methyl-L-arginine; alpha-1-microglobulin-Ig alpha complex chromophore;bis-L-cysteinyl bis-L-histidino diiron disulfide;bis-L-cysteinyl-L-N3′-histidino-L-serinyI tetrairon′ tetrasulfide;chondroitin sulfateD-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine; D-alanine;D-allo-isoleucine; D-asparagine; dehydroalanine; dehydrotyrosine;dermatan 4-sulfateD-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine;D-glucuronyl-N-glycine; dipyrrolylmethanemethyl-L-cysteine; D-leucine;D-methionine; D-phenylalanine; D-serine; D-tryptophan; glycine amide;glycine oxazolecarboxylic acid; glycine thiazolecarboxylic acid; hemeP450-bis-L-cysteine-L-tyrosine; heme-bis-L-cysteine; hemediol-L-aspartylester-L-glutamyl ester, hemediol-L-aspartyl ester-L-glutamylester-L-methionine sulfonium; heme-L-cysteine; heme-L-histidine; heparansulfate D-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-serine; hemeP450-bis-L-cysteine-L-lysine; hexakis-L-cysteinyl hexairon hexasulfide;keratan sulfateD-glucuronyl-D-galactosyl-D-galactosyl-D-xylosyl-L-threonine; Loxoalanine-lactic acid; L phenyllactic acid;1′-(8alpha-FAD)-L-histidine; L-2′.4′,5′-topaquinone;L-3′,4′-dihydroxyphenylalanine; L-3′.4′.5′-trihydroxyphenylalanine;L-4′-bromophenylalanine; L-6′-bromotryptophan; L-alanine amide; L-alanylimidazolinone glycine; L-allysine; L-arginine amide; L-asparagine amide;L-aspartic 4-phosphoric anhydride; L-aspartic acid 1-amide;L-beta-methylthioaspartic acid; L-bromohistidine; L-citrulline;L-cysteine amide; L-cysteine glutathione disulfide; L-cysteine methyldisulfide; L-cysteine methyl ester; L-cysteine oxazolecarboxylic acid;L-cysteine oxazolinecarboxylic acid; L-cysteine persulfide; L-cysteinesulfenic acid; L-cysteine sulfinic acid; L-cysteine thiazolecarboxylicacid; L-cysteinyl homocitryl molybdenum-heptairon-nonasulfide;L-cysteinyl imidazolinone glycine; L-cysteinyl molybdopterin;L-cysteinyl molybdopterin guanine dinucleotide; L-cystine;L-erythro-beta-hydroxyasparagine; L-erythro-beta-hydroxyaspartic acid;L-gamma-carboxyglutamic acid; L-glutamic acid 1-amide; L-glutamic acid5-methyl ester, L-glutamine amide; L-glutamyl5-glycerylphosphorylethanolamine; L-histidine amide;L-isoglutamyl-polyglutamic acid; L-isoglutamyl-polyglycine; L-isoleucineamide; L-lanthionine; L-leucine amide; L-lysine amide; L-lysinethiazolecarboxylic acid; L-lysinoalanine; L-methionine amide;L-methionine sulfone; L-phenyalanine thiazolecarboxylic acid;L-phenylalanine amide; L-proline amide; L-selenocysteine;L-selenocysteinyl molybdopterin guanine dinucleotide; L-serine amide;L-serine thiazolecarboxylic acid; L-seryl imidazolinone glycine;L-T-bromophenylalanine; L-T-bromophenylalanine; L-threonine amide;L-thyroxine; L-tryptophan amide; L-tryptophyl quinone; L-tyrosine amide;L-valine amide; meso-lanthionine; N-(L-glutamyl)-L-tyrosine;N-(L-isoaspartyl)-glycine; N-(L-isoaspartyl)-L-cysteine;N,N,N-trimethyl-L-alanine; N,N-dimethyl-L-proline; N2-acetyl-L-lysine;N2-succinyl-L-tryptophan; N4-(ADP-ribosyl)-L-asparagine;N4-glycosyl-L-asparagine; N4-hydroxymethyl-L-asparagine;N4-methyl-L-asparagine; N5-methyl-L-glutamine;N6-1-carboxyethyl-L-lysine; N6-(4-amino hydroxybutyl)-L-lysine;N6-(L-isoglutamyl)-L-lysine; N6-(phospho-5′-adenosine)-L-lysine;N6-(phospho-5′-guanosine)-L-lysine; N6,N6,N6-trimethyl-L-lysine;N6,N6-dimethyl-L-lysine; N6-acetyl-L-lysine; N6-biotinyl-L-lysine;N6-carboxy-L-lysine; N6-formyl-L-lysine; N6-glycyl-L-lysine;N6-lipoyl-L-lysine; N6-methyl-L-lysine;N6-methyl-N6-poly(N-methyl-propylamine)-L-lysine; N6-mureinyl-L-lysine;N6-myristoyl-L-lysine; N6-palmitoyl-L-lysine; N6-pyridoxalphosphate-L-lysine; N6-pyruvic acid 2-iminyl-L-lysine;N6-retinal-L-lysine; N-acetylglycine; N-acetyl-L-glutamine;N-acetyl-L-alanine; N-acetyl-L-aspartic acid; N-acetyl-L-cysteine;N-acetyl-L-glutamic acid; N-acetyl-L-isoleucine; N-acetyl-L-methionine;N-acetyl-L-proline; N-acetyl-L-serine; N-acetyl-L-threonine;N-acetyl-L-tyrosine; N-acetyl-L-valine;N-alanyl-glycosylphosphatidylinositolethanolamine;N-asparaginyl-glycosylphosphatidylinositolethanolanine;N-aspartyl-glycosylphosphatidylinositolethanolamine; N-formylglycine;N-formyl-L-methionine;N-glycyl-glycosylphosphatidylinositolethanolamine;N-L-glutamyl-poly-L-glutamic acid; N-methylglycine; N-methyl-L-alanine;N-methyl-L-methionine; N-methyl-L-phenylalanine; N-myristoyl-glycine;N-palmitoyl-L-cysteine; N-pyruvic acid 2-iminyl-L-cysteine; N-pyruvicacid 2-iminyl-L-valine;N-seryl-glycosylphosphatidylinositolethanolamine;N-seryl-glycosyOSPhingolipidinositolethanolamine;O-(ADP-ribosyl)-L-serine; O-(phospho-5′-adenosine)-L-threonine;O-(phospho-5′-DNA)-L-serine; O-(phospho-5′-DNA)-L-threonine;O-(phospho-5′rRNA)-L-serine; O-(phosphoribosyl dephospho-coenzymeA)-L-serine; O-(sn-1-glycerophosphoryl)-L-serine;O4′-(8alpha-FAD)-L-tyrosine; O4′-(phospho-5′-adenosine)-L-tyrosine;O4′-(phospho-5′-DNA)-L-tyrosine; O4′-(phospho-5′-RNA)-L-tyrosine;O4′-(phospho-5′-uridine)-L-tyrosine; O4-glycosyl-L-hydroxyproline;O4′-glycosyl-L-tyrosine; O4′-sulfo-L-tyrosine;O5-glycosyl-L-hydroxylysine; O-glycosyl-L-serine;O-glycosyl-L-threonine; omega-N-(ADP-ribosyl)-L-arginine;omega-N-omega-N′-dimethyl-L-arginine; omega-N-methyl-L-arginine;omega-N-omega-N-dimethyl-L-arginine; omega-N-phospho-L-arginine;O′octanoyl-L-serine; O-palmitoyl-L-serine; O-palmitoyl-L-threonine;O-phospho-L-serine; O-phospho-L-threonine;O-phosphopantetheine-L-serine; phycoerythrobilin-bis-L-cysteine;phycourobilin-bis-L-cysteine; pyrroloquinoline quinone; pyruvic acid; Shydroxycinnamyl-L-cysteine; S-(2-aminovinyl)methyl-D-cysteine;S-2-aminovinyl)-D-cysteine; S-(6-FW-L-cysteine;S-(8alpha-FAD)-L-cysteine; S-(ADP-ribosyl)-L-cysteine;S-(L-isoglutamyl)-L-cysteine; S-12-hydroxyfarnesyl-L-cysteine;S-acetyl-L-cysteine; S-diacylglycerol-L-cysteine; S-diphytanylglycerotdiether-L-cysteine; S-farnesyl-L-cysteine; S-geranylgeranyl-L-cysteine;S-glycosyl-L-cysteine; S-glycyl-L-cysteine; S-methyl-L-cysteine;S-nitrosyl-L-cysteine; S-palmitoyl-L-cysteine; S-phospho-L-cysteine;S-phycobiliviolin-L-cysteine; S-phycocyanobilin-L-cysteine;S-phycoerythrobilin-L-cysteine; S-phytochromobilin-L-cysteine;S-selenyl-L-cysteine; S-sulfo-L-cysteine; tetrakis-L-cysteinyl diirondisulfide; tetrakis-L-cysteinyl iron; tetrakis-L-cysteinyl tetrairontetrasulfide; trans-2,3-cis 4-dihydroxy-L-proline; tris-L-cysteinyltriiron tetrasulfide; tris-L-cysteinyl triiron trisulfide;tris-L-cysteinyl-L-aspartato tetrairon tetrasulfide;tris-L-cysteinyl-L-cysteine persulfido-bis-L-glutamato-L-histidinotetrairon disulfide trioxide; tris-L-cysteinyl-L-N3′-histidino tetrairontetrasulfide; tris-L-cysteinyl-L-N1′-histidino tetrairon tetrasulfide;and tris-L-cysteinyl-L-serinyl tetrairon tetrasulfide.

Additional examples of PTMs may be found in web sites such as the DeltaMass database based on Krishna, R. G. and F. Wold (1998).Posttranslational Modifications. Proteins—Analysis and Design. R. H.Angeletti. San Diego, Academic Press. 1: 121-206; Methods in Enzymology,193, J. A. McClosky (ed) (1990), pages 647-660; Methods in ProteinSequence Analysis edited by Kazutomo Imahori and Fumio Sakiyama, PlenumPress, (1993) “Post-translational modifications of proteins” R. G.Krishna and F. Wold pages 167-172; “GlycoSuiteDB: a new curatedrelational database of glycoprotein glycan structures and theirbiological sources” Cooper et al. Nucleic Acids Res. 29; 332-335 (2001)“O-GLYCBASE version 4.0: a revised database of O-glycosylated proteins”Gupta et al. Nucleic Acids Research, 27: 370-372 (1999); and“PhosphoBase, a database of phosphorylation sites: release 2.0.”,Kreegipuu et al. Nucleic Acids Res 27(1):237-239 (1999) see also, WO02/21139A2, the disclosure of which is incorporated herein by referencein its entirety.

Tumorigenesis is often accompanied by alterations in thepost-translational modifications of proteins. Thus, in anotherembodiment, the invention provides polypeptides from cancerous cells ortissues that have altered post-translational modifications compared tothe post-translational modifications of polypeptides from normal cellsor tissues. A number of altered post-translational modifications areknown. One common alteration is a change in phosphorylation state,wherein the polypeptide from the cancerous cell or tissue ishyperphosphorylated or hypophosphorylated compared to the polypeptidefrom a normal tissue, or wherein the polypeptide is phosphorylated ondifferent residues than the polypeptide from a normal cell. Anothercommon alteration is a change in glycosylation state, wherein thepolypeptide from the cancerous cell or tissue has more or lessglycosylation than the polypeptide from a normal tissue, and/or whereinthe polypeptide from the cancerous cell or tissue has a different typeof glycosylation than the polypeptide from a noncancerous cell ortissue. Changes in glycosylation may be critical becausecarbohydrate-protein and carbohydrate-carbohydrate interactions areimportant in cancer cell progression, dissemination and invasion. See,e.g., Barchi, Curr. Pharm. Des. 6: 485-501 (2000), Verma, CancerBiochem. Biophys. 14: 151-162 (1994) and Dennis et al., Bioessays 5:412-421 (1999).

Another post-translational modification that may be altered in cancercells is prenylation. Prenylation is the covalent attachment of ahydrophobic prenyl group (either farnesyl or geranylgeranyl) to apolypeptide. Prenylation is required for localizing a protein to a cellmembrane and is often required for polypeptide function. For instance,the Ras superfamily of GTPase signalling proteins must be prenylated forfunction in a cell. See, e.g., Prendergast et al., Semin. Cancer Biol.10: 443-452 (2000) and Khwaja et al., Lancet 355: 741-744 (2000).

Other post-translation modifications that may be altered in cancer cellsinclude, without limitation, polypeptide methylation, acetylation,arginylation or racemization of amino acid residues. In these cases, thepolypeptide from the cancerous cell may exhibit either increased ordecreased amounts of the post-translational modification compared to thecorresponding polypeptides from noncancerous cells.

Other polypeptide alterations in cancer cells include abnormalpolypeptide cleavage of proteins and aberrant protein-proteininteractions. Abnormal polypeptide cleavage may be cleavage of apolypeptide in a cancerous cell that does not usually occur in a normalcell, or a lack of cleavage in a cancerous cell, wherein the polypeptideis cleaved in a normal cell. Aberrant protein-protein interactions maybe either covalent cross-linking or non-covalent binding betweenproteins that do not normally bind to each other. Alternatively, in acancerous cell, a protein may fail to bind to another protein to whichit is bound in a noncancerous cell. Alterations in cleavage or inprotein-protein interactions may be due to over- or underproduction of apolypeptide in a cancerous cell compared to that in a normal cell, ormay be due to alterations in post-translational modifications (seeabove) of one or more proteins in the cancerous cell. See, e.g.,Henschen-Edman, Ann. N.Y. Acad. Sci. 936: 580-593 (2001).

Alterations in polypeptide post-translational modifications, as well aschanges in polypeptide cleavage and protein-protein interactions, may bedetermined by any method known in the art. For instance, alterations inphosphorylation may be determined by using anti-phosphoserine,anti-phosphothreonine or anti-phosphotyrosine antibodies or by aminoacid analysis. Glycosylation alterations may be determined usingantibodies specific for different sugar residues, by carbohydratesequencing, or by alterations in the size of the glycoprotein, which canbe determined by, e.g., SDS polyacrylamide gel electrophoresis (PAGE).Other alterations of post-translational modifications, such asprenylation, racemization, methylation, acetylation and arginylation,may be determined by chemical analysis, protein sequencing, amino acidanalysis, or by using antibodies specific for the particularpost-translational modifications. Changes in protein-proteininteractions and in polypeptide cleavage may be analyzed by any methodknown in the art including, without limitation, non-denaturing PAGE (fornon-covalent protein-protein interactions), SDS PAGE (for covalentprotein-protein interactions and protein cleavage), chemical cleavage,protein sequencing or immunoassays.

In another embodiment, the invention provides polypeptides that havebeen post-translationally modified. In one embodiment, polypeptides maybe modified enzymatically or chemically, by addition or removal of apost-translational modification. For example, a polypeptide may beglycosylated or deglycosylated enzymatically. Similarly, polypeptidesmay be phosphorylated using a purified kinase, such as a MAP kinase(e.g., p38, ERK, or JNK) or a tyrosine kinase (e.g., Src or erbB2). Apolypeptide may also be modified through synthetic chemistry.Alternatively, one may isolate the polypeptide of interest from a cellor tissue that expresses the polypeptide with the desiredpost-translational modification. In another embodiment, a nucleic acidmolecule encoding the polypeptide of interest is introduced into a hostcell that is capable of post-translationally modifying the encodedpolypeptide in the desired fashion. If the polypeptide does not containa motif for a desired post-translational modification, one may alter thepost-translational modification by mutating the nucleic acid sequence ofa nucleic acid molecule encoding the polypeptide so that it contains asite for the desired post-translational modification. Amino acidsequences that may be post-translationally modified are known in theart. See, e.g., the programs described above on the website expasy.orgof the world wide web. The nucleic acid molecule may also be introducedinto a host cell that is capable of post-translationally modifying theencoded polypeptide. Similarly, one may delete sites that arepost-translationally modified by either mutating the nucleic acidsequence so that the encoded polypeptide does not contain thepost-translational modification motif, or by introducing the nativenucleic acid molecule into a host cell that is not capable ofpost-translationally modifying the encoded polypeptide.

It will be appreciated, as is well known and as noted above, thatpolypeptides are not always entirely linear. For instance, polypeptidesmay be branched as a result of ubiquitination, and they may be circular,with or without branching, generally as a result of posttranslationevents, including natural processing events and events brought about byhuman manipulation which do not occur naturally. Circular, branched andbranched circular polypeptides may be synthesized by non-translationnatural processes and by entirely synthetic methods, as well.Modifications can occur anywhere in a polypeptide, including the peptidebackbone, the amino acid side-chains and the amino or carboxyl termini.In fact, blockage of the amino or carboxyl group in a polypeptide, orboth, by a covalent modification, is common in naturally occurring andsynthetic polypeptides and such modifications may be present inpolypeptides of the present invention, as well. For instance, the aminoterminal residue of polypeptides made in E. coli, prior to proteolyticprocessing, almost invariably will be N-formylmethionine.

Useful post-synthetic (and post-translational) modifications includeconjugation to detectable labels, such as fluorophores. A wide varietyof amine-reactive and thiol-reactive fluorophore derivatives have beensynthesized that react under nondenaturing conditions with N-terminalamino groups and epsilon amino groups of lysine residues, on the onehand, and with free thiol groups of cysteine residues, on the other.

Kits are available commercially that permit conjugation of proteins to avariety of amine-reactive or thiol-reactive fluorophores: MolecularProbes, Inc. (Eugene, Oreg., USA), e.g., offers kits for conjugatingproteins to Alexa Fluor 350, Alexa Fluor 430, Fluorescein-EX, AlexaFluor 488, Oregon Green 488, Alexa Fluor 532, Alexa Fluor 546, AlexaFluor 546, Alexa Fluor 568, Alexa Fluor 594, and Texas Red-X.

A wide variety of other amine-reactive and thiol-reactive fluorophoresare available commercially (Molecular Probes, Inc., Eugene, Oreg., USA),including Alexa Fluor® 350, Alexa Fluor® 488, Alexa Fluor® 532, AlexaFluor® 546, Alexa Fluor® 568, Alexa Fluor® 594, Alexa Fluor® 647(monoclonal antibody labeling kits available from Molecular Probes,Inc., Eugene, Oreg., USA), BODIPY dyes, such as BODIPY 493/503, BODIPYFL, BODIPY R6G, BODIPY 530/550, BODIPY TMR, BODIPY 558/568, BODIPY558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY TR,BODIPY 630/650, BODIPY 650/665, Cascade Blue, Cascade Yellow, Dansyl,lissamine rhodamine B, Marina Blue, Oregon Green 488, Oregon Green 514,Pacific Blue, rhodamine 6G, rhodamine green, rhodamine red,tetramethylrhodamine, Texas Red (available from Molecular Probes, Inc.,Eugene, Oreg., USA).

The polypeptides of the present invention can also be conjugated tofluorophores, other proteins, and other macromolecules, usingbifunctional linking reagents. Common homobifunctional reagents include,e.g., APG, AEDP, BASED, BMB, BMDB, BMH, BMOE, BM[PEO]3, BM[PEO]4, BS3,BSOCOES, DFDNB, DMA, DMP, DMS, DPDPB, DSG, DSP (Lomant's Reagent), DSS,DST, DTBP, DTME, DTSSP, EGS, HBVS, Sulfo-BSOCOES, Sulfo-DST, Sulfo-EGS(all available from Pierce, Rockford, Ill., USA); commonheterobifunctional cross-linkers include ABH, AMAS, ANB-NOS, APDP, ASBA,BMPA, BMPH, BMPS, EDC, EMCA, EMCH, EMCS, KMUA, KMUH, GMBS, LC-SMCC,LC-SPDP, MBS, M2C2H, MPBH, MSA, NHS-ASA, PDPH, PMPI, SADP, SAED, SAND,SANPAH, SASD, SATP, SBAP, SFAD, SIA, SIAB, SMCC, SMPB, SMPH, SMPT, SPDP,Sulfo-EMCS, Sulfo-GMBS, Sulfo-HSAB, Sulfo-KMUS, Sulfo-LC-SPDP,Sulfo-MBS, Sulfo-NHS-LC-ASA, Sulfo-SADP, Sulfo-SANPAH, Sulfo-SIAB,Sulfo-SMCC, Sulfo-SMPB, Sulfo-LC-SMPT, SVSB, TFCS (all available Pierce,Rockford, Ill., USA).

Polypeptides of the present invention, including full lengthpolypeptides, fragments and fusion proteins, can be conjugated, usingsuch cross-linking reagents, to fluorophores that are not amine- orthiol-reactive. Other labels that usefully can be conjugated topolypeptides of the present invention include radioactive labels,echosonographic contrast reagents, and MRI contrast agents.

Polypeptides of the present invention, including full lengthpolypeptides, fragments and fusion proteins, can also usefully beconjugated using cross-linking agents to carrier proteins, such as KLH,bovine thyroglobulin, and even bovine serum albumin (BSA), to increaseimmunogenicity for raising anti-OSP antibodies.

Polypeptides of the present invention, including fall lengthpolypeptides, fragments and fusion proteins, can also usefully beconjugated to polyethylene glycol (PEG); PEGylation increases the serumhalf life of proteins administered intravenously for replacementtherapy. Delgado et al., Crit. Rev. Ther. Drug Carrier Syst. 9(3-4):249-304 (1992); Scott et al., Curr. Pharm. Des. 4(6): 423-38 (1998);DeSantis et al., Curr. Opin. Biotechnol. 10(4): 324-30 (1999). PEGmonomers can be attached to the protein directly or through a linker,with PEGylation using PEG monomers activated with tresyl chloride(2,2,2-trifluoroethanesulphonyl chloride) permitting direct attachmentunder mild conditions.

Polypeptides of the present invention are also inclusive of analogs of apolypeptide encoded by a nucleic acid molecule according to the instantinvention. In a preferred embodiment, this polypeptide is an OSP. In amore preferred embodiment, this polypeptide is derived from apolypeptide having part or all of the amino acid sequence of SEQ ID NO:129-295. Also preferred is an analog polypeptide comprising one or moresubstitutions of non-natural amino acids or non-native inter-residuebonds compared to the naturally occurring polypeptide. In oneembodiment, the analog is structurally similar to an OSP, but one ormore peptide linkages is replaced by a linkage selected from the groupconsisting of —CH₂NH—, —CH₂S—, —CH₂—CH₂—, —CH═CH-(cis and trans),—COCH₂—, —CH(OH)CH₂— and —CH₂SO—. In another embodiment, the analogcomprises substitution of one or more amino acids of an OSP with aD-amino acid of the same type or other non-natural amino acid in orderto generate more stable peptides. D-amino acids can readily beincorporated during chemical peptide synthesis: peptides assembled fromD-amino acids are more resistant to proteolytic attack; incorporation ofD-amino acids can also be used to confer specific three-dimensionalconformations on the peptide. Other amino acid analogues commonly addedduring chemical synthesis include ornithine, norleucine, phosphorylatedamino acids (typically phosphoserine, phosphothreonine,phosphotyrosine), L-malonyltyrosine, a non-hydrolyzable analog ofphosphotyrosine (see, e.g., Kole et al., Biochem. Biophys. Res. Com.209: 817-821 (1995)), and various halogenated phenylalanine derivatives.

Non-natural amino acids can be incorporated during solid phase chemicalsynthesis or by recombinant techniques, although the former is typicallymore common. Solid phase chemical synthesis of peptides is wellestablished in the art. Procedures are described, inter alia, in Chan etal. (eds.), Fmoc Solid Phase Peptide Synthesis: A Practical Approach(Practical Approach Series), Oxford Univ. Press (March 2000); Jones,Amino Acid and Peptide Synthesis (Oxford Chemistry Primers, No 7),Oxford Univ. Press (1992); and Bodanszky, Principles of PeptideSynthesis (Springer Laboratory), Springer Verlag (1993).

Amino acid analogues having detectable labels are also usefullyincorporated during synthesis to provide derivatives and analogs.Biotin, for example can be added usingbiotinoyl-(9-fluorenylmethoxycarbonyl)-L-lysine (FMOC biocytin)(Molecular Probes, Eugene, Oreg., USA). Biotin can also be addedenzymatically by incorporation into a fusion protein of an E. coli BirAsubstrate peptide. The FMOC and tBOC derivatives of dabcyl-L-lysine(Molecular Probes, Inc., Eugene, Oreg., USA) can be used to incorporatethe dabcyl chromophore at selected sites in the peptide sequence duringsynthesis. The aminonaphthalene derivative EDANS, the most commonfluorophore for pairing with the dabcyl quencher in fluorescenceresonance energy transfer (FRET) systems, can be introduced duringautomated synthesis of peptides by using EDANS-FMOC-L-glutamic acid orthe corresponding tBOC derivative (both from Molecular Probes, Inc.,Eugene, Oreg., USA). Tetramethylrhodamine fluorophores can beincorporated during automated FMOC synthesis of peptides using(FMOC)-TMR-L-lysine (Molecular Probes, Inc. Eugene, Oreg., USA).

Other useful amino acid analogues that can be incorporated duringchemical synthesis include aspartic acid, glutamic acid, lysine, andtyrosine analogues having allyl side-chain protection (AppliedBiosystems, Inc., Foster City, Calif., USA); the allyl side chainpermits synthesis of cyclic, branched-chain, sulfonated, glycosylated,and phosphorylated peptides.

A large number of other FMOC-protected non-natural amino acid analoguescapable of incorporation during chemical synthesis are availablecommercially, including, e.g.,Fmoc-2-aminobicyclo[2.2.1]heptane-2-carboxylic acid,Fmoc-3-endo-aminobicyclo[2.2.1]heptane-2-endo-carboxylic acid,Fmoc-3-exo-aminobicyclo[2.2.1]heptane-2-exo-carboxylic acid,Fmoc-3-endo-amino-bicyclo[2.2.1]hept-5-ene-2-endo-carboxylic acid,Fmoc-3-exo-amino-bicyclo[2.2.1]hept-5-ene-2-exo-carboxylic acid,Fmoc-cis-2-amino-1-cyclohexanecarboxylic acid,Fmoc-trans-2-amino-1-cyclohexanecarboxylic acid,Fmoc-1-amino-1-cyclopentanecarboxylic acid,Fmoc-cis-2-amino-1-cyclopentanecarboxylic acid,Fmoc-1-amino-1-cyclopropanecarboxylic acid,Fmoc-D-2-amino4-(ethylthio)butyric acid,Fmoc-L-2-amino-4-(ethylthio)butyric acid, Fmoc-L-buthionine,Fmoc-S-methyl-L-Cysteine, Fmoc-2-aminobenzoic acid (anthranillic acid),Fmoc-3-aminobenzoic acid, Fmoc-4-aminobenzoic acid,Fmoc-2-aminobenzophenone-2′-carboxylic acid,Fmoc-N-(4-aminobenzoyl)-β-alanine, Fmoc-2-amino-4,5-dimethoxybenzoicacid, Fmoc-4-aminohippuric acid, Fmoc-2-amino-3-hydroxybenzoic acid,Fmoc-2-amino-5-hydroxybenzoic acid, Fmoc-3-amino-4-hydroxybeznoic acid,Fmoc-4-amino-3-hydroxybenzoic acid, Fmoc-4-amino-2-hydroxybenzoic acid,Fmoc-5-amino-2-hydroxybenzoic acid, Fmoc-2-amino-3-methoxybenzoic acid,Fmoc-4-amino-3-methoxybenzoic acid, Fmoc-2-amino-3-methylbenzoic acid,Fmoc-2-amino-5-methylbenzoic acid, Fmoc-2-amino-6-methylbenzoic acid,Fmoc-3-amino-2-methylbenzoic acid, Fmoc-3-amino4-methylbenzoic acid,Fmoc-4-amino-3-methylbenzoic acid, Fmoc-3-amino-2-naphtoic acid,Fmoc-D,L-3-amino-3-phenylpropionic acid, Fmoc-L-Methyldopa,Fmoc-2-amino-4,6-dimethyl-3-pyridinecarboxylic acid,Fmoc-D,L-amino-2-thiophenacetic acid, Fmoc-4-(carboxymethyl)piperazine,Fmoc-4-carboxypiperazine, Fmoc-4-(carboxymethyl)homopiperazine,Fmoc-4-phenyl-4-piperidinecarboxylic acid,Fmoc-L-1,2,3,4-tetrahydronorharman-3-carboxylic acid,Fmoc-L-thiazolidine-4-carboxylic acid, all available from The PeptideLaboratory (Richmond, Calif., USA).

Non-natural residues can also be added biosynthetically by engineering asuppressor tRNA, typically one that recognizes the UAG stop codon, bychemical aminoacylation with the desired unnatural amino acid.Conventional site-directed mutagenesis is used to introduce the chosenstop codon UAG at the site of interest in the protein gene. When theacylated suppressor tRNA and the mutant gene are combined in an in vitrotranscription/translation system, the unnatural amino acid isincorporated in response to the UAG codon to give a protein containingthat amino acid at the specified position. Liu et al, Proc. Natl Acad.Sci. USA 96(9): 4780-5 (1999); Wang et al., Science 292(5516): 498-500(2001).

Fusion Proteins

Another aspect of the present invention relates to the fusion of apolypeptide of the present invention to heterologous polypeptides. In apreferred embodiment, the polypeptide of the present invention is anOSP. In a more preferred embodiment, the polypeptide of the presentinvention that is fused to a heterologous polypeptide which comprisespart or all of the amino acid sequence of SEQ ID NO: 129-295, or is amutein, homologous polypeptide, analog or derivative thereof. In an evenmore preferred embodiment, the fusion protein is encoded by a nucleicacid molecule comprising all or part of the nucleic acid sequence of SEQID NO: 1-128, or comprises all or part of a nucleic acid sequence thatselectively hybridizes or is homologous to a nucleic acid moleculecomprising a nucleic acid sequence of SEQ ID NO: 1-128.

The fusion proteins of the present invention will include at least onefragment of a polypeptide of the present invention, which fragment is atleast 6, typically at least 8, often at least 15, and usefully at least16, 17, 18, 19, or 20 amino acids long. The fragment of the polypeptideof the present to be included in the fusion can usefully be at least 25amino acids long, at least 50 amino acids long, and can be at least 75,100, or even 150 amino acids long. Fusions that include the entirety ofa polypeptide of the present invention have particular utility.

The heterologous polypeptide included within the fusion protein of thepresent invention is at least 6 amino acids in length, often at least 8amino acids in length, and preferably at least 15, 20, or 25 amino acidsin length. Fusions that include larger polypeptides, such as the IgG Fcregion, and even entire proteins (such as GFP chromophore-containingproteins) are particularly useful.

As described above in the description of vectors and expression vectorsof the present invention, which discussion is incorporated here byreference in its entirety, heterologous polypeptides to be included inthe fusion proteins of the present invention can usefully include thosedesigned to facilitate purification and/or visualization ofrecombinantly-expressed proteins. See, e.g., Ausubel, Chapter 16,(1992), supra. Although purification tags can also be incorporated intofusions that are chemically synthesized, chemical synthesis typicallyprovides sufficient purity that further purification by HPLC suffices;however, visualization tags as above described retain their utility evenwhen the protein is produced by chemical synthesis, and when so includedrender the fusion proteins of the present invention useful as directlydetectable markers of the presence of a polypeptide of the invention.

As also discussed above, heterologous polypeptides to be included in thefusion proteins of the present invention can usefully include those thatfacilitate secretion of recombinantly expressed proteins into theperiplasmic space or extracellular milieu for prokaryotic hosts or intothe culture medium for eukaryotic cells through incorporation ofsecretion signals and/or leader sequences. For example, a His6 taggedprotein can be purified on a Ni affinity column and a GST fusion proteincan be purified on a glutathione affinity column. Similarly, a fusionprotein comprising the Fc domain of IgG can be purified on a Protein Aor Protein G column and a fusion protein comprising an epitope tag suchas myc can be purified using an immunoaffinity column containing ananti-c-myc antibody. It is preferable that the epitope tag be separatedfrom the protein encoded by the essential gene by an enzymatic cleavagesite that can be cleaved after purification. See also the discussion ofnucleic acid molecules encoding fusion proteins that may be expressed onthe surface of a cell.

Other useful fusion proteins of the present invention include those thatpermit use of the polypeptide of the present invention as bait in ayeast two-hybrid system. See Bartel et al. (eds.), The Yeast Two-HybridSystem, Oxford University Press (1997); Zhu et al., Yeast HybridTechnologies Eaton Publishing (2000); Fields et al., Trends Genet.10(8): 286-92 (1994); Mendelsohn et al., Curr. Opin. Biotechnol. 5(5):482-6 (1994); Luban et al., Curr. Opin. Biotechnol. 6(1): 59-64 (1995);Allen et al., Trends Biochem. Sci. 20(12): 511-6 (1995); Drees, Curr.Opin. Chem. Biol. 3(1): 64-70 (1999); Topcu et al., Pharm. Res. 17(9):1049-55 (2000); Fashena et al., Gene 250(1-2): 1-14 (2000); Colas etal., Nature 380, 548-550 (1996); Norman, T. et al., Science 285, 591-595(1999); Fabbrizio et al., Oncogene 18, 4357-4363 (1999); Xu et al., ProcNatl Acad Sci USA. 94, 12473-12478 (1997); Yang, et al., Nuc. Acids Res.23, 1152-1156 (1995); Kolonin et al., Proc Natl Acad Sci USA 95,14266-14271 (1998); Cohen et al., Proc Natl Acad Sci USA 95, 14272-14277(1998); Uetz, et al. Nature 403, 623-627(2000); Ito, et al., Proc NatlAcad Sci USA 98, 4569-4574 (2001). Typically, such fusion is to eitherE. coli LexA or yeast GAL4 DNA binding domains. Related bait plasmidsare available that express the bait fused to a nuclear localizationsignal.

Other useful fusion proteins include those that permit display of theencoded polypeptide on the surface of a phage or cell, fusions tointrinsically fluorescent proteins, such as green fluorescent protein(GFP), and fusions to the IgG Fc region, as described above.

The polypeptides of the present invention can also usefully be fused toprotein toxins, such as Pseudomonas exotoxin A, diphtheria toxin, shigatoxin A, anthrax toxin lethal factor, or ricin, in order to effectablation of cells that bind or take up the proteins of the presentinvention.

Fusion partners include, inter alia, myc, hemagglutinin (HA), GST,immunoglobulins, β-galactosidase, biotin trpE, protein A, β-lactamase,α-amylase, maltose binding protein, alcohol dehydrogenase, polyhistidine(for example, six histidine at the amino and/or carboxyl terminus of thepolypeptide), lacZ, green fluorescent protein (GFP), yeast α matingfactor, GAL4 transcription activation or DNA binding domain, luciferase,and serum proteins such as ovalbumin, albumin and the constant domain ofIgG. See, e.g., Ausubel (1992), supra and Ausubel (1999), supra. Fusionproteins may also contain sites for specific enzymatic cleavage, such asa site that is recognized by enzymes such as Factor XIII, trypsin,pepsin, or any other enzyme known in the art. Fusion proteins willtypically be made by either recombinant nucleic acid methods, asdescribed above, chemically synthesized using techniques well known inthe art (e.g., a Merrifield synthesis), or produced by chemicalcross-linking.

Another advantage of fusion proteins is that the epitope tag can be usedto bind the fusion protein to a plate or column through an affinitylinkage for screening binding proteins or other molecules that bind tothe OSP.

As further described below, the polypeptides of the present inventioncan readily be used as specific immunogens to raise antibodies thatspecifically recognize polypeptides of the present invention includingOSPs and their allelic variants and homologues. The antibodies, in turn,can be used, inter alia, specifically to assay for the polypeptides ofthe present invention, particularly OSPs, e.g. by ELISA for detection ofprotein fluid samples, such as serum, by immunohistochemistry or laserscanning cytometry, for detection of protein in tissue samples, or byflow cytometry, for detection of intracellular protein in cellsuspensions, for specific antibody-mediated isolation and/orpurification of OSPs, as for example by immunoprecipitation, and for useas specific agonists or antagonists of OSPs.

One may determine whether polypeptides of the present inventionincluding OSPs, muteins, homologous proteins or allelic variants orfusion proteins of the present invention are functional by methods knownin the art. For instance, residues that are tolerant of change whileretaining function can be identified by altering the polypeptide atknown residues using methods known in the art, such as alanine scanningmutagenesis, Cunningham et al., Science 244(4908): 1081-5 (1989);transposon linker scanning mutagenesis, Chen et al., Gene 263(1-2):39-48 (2001); combinations of homolog- and alanine-scanning mutagenesis,Jin et al., J. Mol. Biol. 226(3): 851-65 (1992); and combinatorialalanine scanning, Weiss et al., Proc. Natl. Acad. Sci USA 97(16): 8950-4(2000), followed by functional assay. Transposon linker scanning kitsare available commercially (New England Biolabs, Beverly, Mass., USA,catalog. no. E7-102S; EZ::TN™ In-Frame Linker Insertion Kit, catalogueno. EZI04KN, (Epicentre Technologies Corporation, Madison, Wisc., USA).

Purification of the polypeptides or fusion proteins of the presentinvention is well known and within the skill of one having ordinaryskill in the art See, e.g., Scopes, Protein Purification. 2d ed. (1987).Purification of recombinantly expressed polypeptides is described above.Purification of chemically-synthesized peptides can readily be effected,e.g., by HPLC.

Accordingly, it is an aspect of the present invention to provide theisolated polypeptides or fusion proteins of the present invention inpure or substantially pure form in the presence or absence of astabilizing agent. Stabilizing agents include both proteinaceous andnon-proteinaceous material and are well known in the art. Stabilizingagents, such as albumin and polyethylene glycol (PEG) are known and arecommercially available.

Although high levels of purity are preferred when the isolatedpolypeptide or fusion protein of the present invention are used astherapeutic agents, such as in vaccines and replacement therapy, theisolated polypeptides of the present invention are also useful at lowerpurity. For example, partially purified polypeptides of the presentinvention can be used as immunogens to raise antibodies in laboratoryanimals.

In a preferred embodiment, the purified and substantially purifiedpolypeptides of the present invention are in compositions that lackdetectable ampholytes, acrylamide monomers, bis-acrylamide monomers, andpolyacrylamide.

The polypeptides or fusion proteins of the present invention canusefully be attached to a substrate. The substrate can be porous orsolid, planar or non-planar; the bond can be covalent or noncovalent.For example, the peptides of the invention may be stabilized by covalentlinkage to albumin. See, U.S. Pat. No. 5,876,969, the contents of whichare hereby incorporated in its entirety.

The polypeptides or fusion proteins of the present invention can also beusefully bound to a porous substrate, commonly a membrane, typicallycomprising nitrocellulose, polyvinylidene fluoride (PVDF), orcationically derivatized, hydrophilic PVDF; so bound, the polypeptidesor fusion proteins of the present invention can be used to detect andquantify antibodies, e.g. in serum, that bind specifically to theimmobilized polypeptide or fusion protein of the present invention.

As another example, the polypeptides or fusion proteins of the presentinvention can usefully be bound to a substantially nonporous substrate,such as plastic, to detect and quantify antibodies, e.g. in serum, thatbind specifically to the immobilized protein of the present invention.Such plastics include polymethylacrylic, polyethylene, polypropylene,polyacrylate, polymethylmethacrylate, polyvinylchloride,polytetrafluoroethylene, polystyrene, polycarbonate, polyacetal,polysulfone, celluloseacetate, cellulosenitrate, nitrocellulose, ormixtures thereof; when the assay is performed in a standard microtiterdish, the plastic is typically polystyrene.

The polypeptides and fusion proteins of the present invention can alsobe attached to a substrate suitable for use as a surface enhanced laserdesorption ionization source; so attached, the polypeptide or fusionprotein of the present invention is useful for binding and thendetecting secondary proteins that bind with sufficient affinity oravidity to the surface-bound polypeptide or fusion protein to indicatebiologic interaction there between. The polypeptides or fusion proteinsof the present invention can also be attached to a substrate suitablefor use in surface plasmon resonance detection; so attached, thepolypeptide or fusion protein of the present invention is useful forbinding and then detecting secondary proteins that bind with sufficientaffinity or avidity to the surface-bound polypeptide or fusion proteinto indicate biological interaction there between.

Alternative Transcripts

In another aspect, the present invention provides splice variants ofgenes and proteins encoded thereby. The identification of a novel splicevariant which encodes an amino acid sequence with a novel region can betargeted for the generation of reagents for use in detection and/ortreatment of cancer. The novel amino acid sequence may lead to a uniqueprotein structure, protein subcellular localization, biochemicalprocessing or function of the splice variant. This information can beused to directly or indirectly facilitate the generation of additionalor novel therapeutics or diagnostics. The nucleotide sequence in thisnovel splice variant can be used as a nucleic acid probe for thediagnosis and/or treatment of cancer.

Specifically, the newly identified sequences may enable the productionof new antibodies or compounds directed against the novel region for useas a therapeutic or diagnostic. Alternatively, the newly identifiedsequences may alter the biochemical or biological properties of theencoded protein in such a way as to enable the generation of improved ordifferent therapeutics targeting this protein.

Antibodies

In another aspect, the invention provides antibodies, includingfragments and derivatives thereof, that bind specifically topolypeptides encoded by the nucleic acid molecules of the invention. Ina preferred embodiment, the antibodies are specific for a polypeptidethat is an OSP, or a fragment, mutein, derivative, analog or fusionprotein thereof. In a more preferred embodiment, the antibodies arespecific for a polypeptide that comprises SEQ ID NO: 129-295, or afragment, mutein, derivative, analog or fusion protein thereof.

The antibodies of the present invention can be specific for linearepitopes, discontinuous epitopes, or conformational epitopes of suchproteins or protein fragments, either as present on the protein in itsnative conformation or, in some cases, as present on the proteins asdenatured, as, e.g., by solubilization in SDS. New epitopes may also bedue to a difference in post translational modifications (PTMs) indisease versus normal tissue. For example, a particular site on an OSPmay be glycosylated in cancerous cells, but not glycosylated in normalcells or vice versa. In addition, alternative splice forms of an OSP maybe indicative of cancer. Differential degradation of the C or N-terminusof an OSP may also be a marker or target for anticancer therapy. Forexample, an OSP may be N-terminal degraded in cancer cells exposing newepitopes to antibodies which may selectively bind for diagnostic ortherapeutic uses.

As is well known in the art, the degree to which an antibody candiscriminate among molecular species in a mixture will depend, in part,upon the conformational relatedness of the species in the mixture;typically, the antibodies of the present invention will discriminateover adventitious binding to non-OSP polypeptides by at least two-fold,more typically by at least 5-fold, typically by more than 10-fold,25-fold, 50-fold, 75-fold, and often by more than 100-fold, and onoccasion by more than 500-fold or 1000-fold. When used to detect theproteins or protein fragments of the present invention, the antibody ofthe present invention is sufficiently specific when it can be used todetermine the presence of the polypeptide of the present invention insamples derived from human ovarian.

Typically, the affinity or avidity of an antibody (or antibody multimer,as in the case of an IgM pentamer) of the present invention for aprotein or protein fragment of the present invention will be at leastabout 1×10⁶ molar (M), typically at least about 5×10⁻⁷ M, 1×10−7 M, withaffinities and avidities of at least 1×10⁻⁸ M, 5×10⁻⁹ M, 1×10⁻¹⁰ M andup to 1×10⁻¹³ M proving especially useful.

The antibodies of the present invention can be naturally occurringforms, such as IgG, IgM, IgD, IgE, IgY, and IgA, from any avian,reptilian, or mammalian species.

Human antibodies can, but will infrequently, be drawn directly fromhuman donors or human cells. In such case, antibodies to thepolypeptides of the present invention will typically have resulted fromfortuitous immunization, such as autoimmune immunization, with thepolypeptide of the present invention. Such antibodies will typically,but will not invariably, be polyclonal. In addition, individualpolyclonal antibodies may be isolated and cloned to generatemonoclonals.

Human antibodies are more frequently obtained using transgenic animalsthat express human immunoglobulin genes, which transgenic animals can beaffirmatively immunized with the protein immunogen of the presentinvention. Human Ig-transgenic mice capable of producing humanantibodies and methods of producing human antibodies therefrom uponspecific immunization are described, inter alia, in U.S. Pat. Nos.6,162,963; 6,150,584; 6,114,598; 6,075,181; 5,939,598; 5,877,397;5,874,299; 5,814,318; 5,789,650; 5,770,429; 5,661,016; 5,633,425;5,625,126; 5,569,825; 5,545,807; 5,545,806, and 5,591,669, thedisclosures of which are incorporated herein by reference in theirentireties. Such antibodies are typically monoclonal, and are typicallyproduced using techniques developed for production of murine antibodies.

Human antibodies are particularly useful, and often preferred, when theantibodies of the present invention are to be administered to humanbeings as in vivo diagnostic or therapeutic agents, since recipientimmune response to the administered antibody will often be substantiallyless than that occasioned by administration of an antibody derived fromanother species, such as mouse.

IgG, IgM, IgD, IgE, IgY, and IgA antibodies of the present invention arealso usefully obtained from other species, including mammals such asrodents (typically mouse, but also rat, guinea pig, and hamster),lagomorphs (typically rabbits), and also larger mammals, such as sheep,goats, cows, and horses; or egg laying birds or reptiles such aschickens or alligators. In such cases, as with the transgenichuman-antibody-producing non-human mammals, fortuitous immunization isnot required, and the non-human mammal is typically affirmativelyimmunized, according to standard immunization protocols, with thepolypeptide of the present invention. One form of avian antibodies maybe generated using techniques described in WO 00/29444, published 25 May2000, which is herein incorporated by reference in its entirety.

As discussed above, virtually all fragments of 8 or more contiguousamino acids of a polypeptide of the present invention can be usedeffectively as immunogens when conjugated to a carrier, typically aprotein such as bovine thyroglobulin, keyhole limpet hemocyanin, orbovine serum albumin, conveniently using a bifunctional linker such asthose described elsewhere above, which discussion is incorporated byreference here.

Immunogenicity can also be conferred by fusion of the polypeptide of thepresent invention to other moieties. For example, polypeptides of thepresent invention can be produced by solid phase synthesis on a branchedpolylysine core matrix; these multiple antigenic peptides (MAPs) providehigh purity, increased avidity, accurate chemical definition andimproved safety in vaccine development. Tam et al., Proc. Natl. Acad.Sci. USA 85: 5409-5413 (1988); Posnett et al., J. Biol. Chem. 263:1719-1725 (1988).

Protocols for immunizing non-human mammals or avian species arewell-established in the art. See Harlow et al. (eds.), Using Antibodies:A Laboratory Manual, Cold Spring Harbor Laboratory (1998); Coligan etal. (eds.), Current Protocols in Immunology, John Wiley & Sons, Inc.(2001); Zola, Monoclonal Antibodies: Preparation and Use of MonoclonalAntibodies and Engineered Antibody Derivatives (Basics: From Backgroundto Bench), Springer Verlag (2000); Gross M, Speck J. Dtsch. Tierarztl.Wochenschr. 103: 417422 (1996). Immunization protocols often includemultiple immunizations, either with or without adjuvants such asFreund's complete adjuvant and Freund's incomplete adjuvant, and mayinclude naked DNA immunization. Moss, Semin. Immunol. 2: 317-327 (1990).

Antibodies from non-human mammals and avian species can be polyclonal ormonoclonal, with polyclonal antibodies having certain advantages inimmunohistochemical detection of the polypeptides of the presentinvention and monoclonal antibodies having advantages in identifying anddistinguishing particular epitopes of the polypeptides of the presentinvention. Antibodies from avian species may have particular advantagein detection of the polypeptides of the present invention, in humanserum or tissues. Vikinge et al., Biosens. Bioelectron. 13: 1257-1262(1998). Following immunization, the antibodies of the present inventioncan be obtained using any art-accepted technique. Such techniques arewell known in the art and are described in detail in references such asColigan, supra; Zola, supra; Howard et al. (eds.), Basic Methods inAntibody Production and Characterization, CRC Press (2000); Harlow,supra; Davis (ed.), Monoclonal Antibody Protocols, Vol. 45, Humana Press(1995); Delves (ed.), Antibody Production: Essential Techniques, JohnWiley & Son Ltd (1997); and Kenney, Antibody Solution: An AntibodyMethods Manual, Chapman & Hall (1997).

Briefly, such techniques include, inter alia, production of monoclonalantibodies by hybridomas and expression of antibodies or fragments orderivatives thereof from host cells engineered to express immunoglobulingenes or fragments thereof. These two methods of production are notmutually exclusive: genes encoding antibodies specific for thepolypeptides of the present invention can be cloned from hybridomas andthereafter expressed in other host cells. Nor need the two necessarilybe performed together: e.g., genes encoding antibodies specific for thepolypeptides of the present invention can be cloned directly from Bcells known to be specific for the desired protein, as further describedin U.S. Pat. No. 5,627,052, the disclosure of which is incorporatedherein by reference in its entirety, or from antibody-displaying phage.

Recombinant expression in host cells is particularly useful whenfragments or derivatives of the antibodies of the present invention aredesired.

Host cells for recombinant antibody production of whole antibodies,antibody fragments, or antibody derivatives can be prokaryotic oreukaryotic.

Prokaryotic hosts are particularly useful for producing phage displayedantibodies of the present invention.

The technology of phage-displayed antibodies, in which antibody variableregion fragments are fused, for example, to the gene III protein (pIII)or gene VIII protein (VIII) for display on the surface of filamentousphage, such as M13, is by now well-established. See, e.g., Sidhu, Curr.Opin. Biotechnol. 11(6): 610-6 (2000); Griffiths et al., Curr. Opin.Biotechnol. 9(1): 102-8 (1998); Hoogenboom et al., Immunotechnology,4(1): 1-20 (1998); Rader et al., Current Opinion in Biotechnology 8:503-508 (1997); Aujame et al., Human Antibodies 8: 155-168 (1997);Hoogenboom, Trends in Biotechnol. 15: 62-70 (1997); de Kruif et al., 17:453-455 (1996); Barbas et al., Trends in Biotechnol. 14: 230-234 (1996);Winter et al., Ann. Rev. Immunol. 433-455 (1994). Techniques andprotocols required to generate, propagate, screen (pan), and use theantibody fragments from such libraries have recently been compiled. See,e.g., Barbas (2001), supra; Kay, supra; and Abelson, supra.

Typically, phage-displayed antibody fragments are scFv fragments or Fabfragments; when desired, full length antibodies can be produced bycloning the variable regions from the displaying phage into a completeantibody and expressing the full length antibody in a furtherprokaryotic or a eukaryotic host cell. Eukaryotic cells are also usefulfor expression of the antibodies, antibody fragments, and antibodyderivatives of the present invention. For example, antibody fragments ofthe present invention can be produced in Pichia pastoris and inSaccharomyces cerevisiae. See, e.g. Takahashi et al., Biosci.Biotechnol. Biochem. 64(10): 2138-44 (2000); Freyre et al., J.Biotechnol. 76(2-3):1 57-63 (2000); Fischer et al., Biotechnol. Appl.Biochem. 30 (Pt 2): 117-20 (1999); Pennell et al., Res. Immunol. 149(6):599-603 (1998); Eldin et al., J. Immunol. Methods. 201(1): 67-75 (1997);Frenken et al., Res. Immunol. 149(6): 589-99 (1998); and Shusta et al.,Nature Biotechnol. 16(8): 773-7 (1998).

Antibodies, including antibody fragments and derivatives, of the presentinvention can also be produced in insect cells. See, e.g., Li et al.,Protein Expr. Purif. 21(1): 121-8 (2001); Ailor et al., Biotechnol.Bioeng. 58(2-3): 196-203 (1998); Hsu et al., Biotechnol. Prog. 13(1):96-104 (1997); Edelman et al., Immunology 91(1): 13-9 (1997); and Nesbitet al., J. Immunol. Methods 151(1-2): 201-8 (1992).

Antibodies and fragments and derivatives thereof of the presentinvention can also be produced in plant cells, particularly maize ortobacco, Giddings et al., Nature Biotechnol. 18(11): 1151-5 (2000);Gavilondo et al, Biotechniques 29(1): 128-38 (2000); Fischer et al., J.Biol. Regul. Homeost. Agents 14(2): 83-92 (2000); Fischer et al.,Biotechnol. Appl. Biochem. 30 (Pt 2): 113-6 (1999); Fischer et al.,Biol. Chem. 380(7-8): 825-39 (1999); Russell, Curr. Top. Microbiol.Immunol. 240: 119-38 (1999); and Ma et al., Plant Physiol. 109(2): 341-6(1995).

Antibodies, including antibody fragments and derivatives, of the presentinvention can also be produced in transgenic, non-human, mammalian milk.See, e.g. Pollock et al., J. Immunol Methods. 231: 147-57 (1999); Younget al., Res. Immunol. 149: 609-10 (1998); and Limonta et al.,Immunotechnology 1: 107-13 (1995).

Mammalian cells useful for recombinant expression of antibodies,antibody fragments, and antibody derivatives of the present inventioninclude CHO cells, COS cells, 293 cells, and myeloma cells. Verma etal., J. Immunol. Methods 216(1-2):165-81 (1998) review and comparebacterial, yeast, insect and mammalian expression systems for expressionof antibodies. Antibodies of the present invention can also be preparedby cell free translation, as further described in Merk et al., J.Biochem. (Tokyo) 125(2): 328-33 (1999) and Ryabova et al., NatureBiotechnol. 15(1): 79-84 (1997), and in the milk of transgenic animals,as further described in Pollock et al., J. Immunol. Methods 231(1-2):147-57 (1999).

The invention further provides antibody fragments that bind specificallyto one or more of the polypeptides of the present invention or to one ormore of the polypeptides encoded by the isolated nucleic acid moleculesof the present invention, or the binding of which can be competitivelyinhibited by one or more of the polypeptides of the present invention orone or more of the polypeptides encoded by the isolated nucleic acidmolecules of the present invention. Among such useful fragments are Fab,Fab′, Fv, F(ab)′₂, and single-chain Fv (scFv) fragments. Other usefulfragments are described in Hudson, Curr. Opin. Biotechnol. 9(4): 395-402(1998).

The present invention also relates to antibody derivatives that bindspecifically to one or more of the polypeptides of the presentinvention, to one or more of the polypeptides encoded by the isolatednucleic acid molecules of the present invention, or the binding of whichcan be competitively inhibited by one or more of the polypeptides of thepresent invention or one or more of the polypeptides encoded by theisolated nucleic acid molecules of the present invention.

Among such useful derivatives are chimeric, primatized, and humanizedantibodies; such derivatives are less immunogenic in human beings, andthus are more suitable for in vivo administration, than are unmodifiedantibodies from non-human mammalian species. Another useful method isPEGylation to increase the serum half life of the antibodies.

Chimeric antibodies typically include heavy and/or light chain variableregions (including both CDR and framework residues) of immunoglobulinsof one species, typically mouse, fused to constant regions of anotherspecies, typically human. See, e.g., Morrison et al., Proc. Natl. Acad.Sci USA.81(21): 6851-5 (1984); Sharon et al., Nature 309(5966): 364-7(1984); Takeda et al., Nature 314(6010): 452-4 (1985); and U.S. Pat. No.5,807,715 the disclosure of which is incorporated herein by reference inits entirety. Primatized and humanized antibodies typically includeheavy and/or light chain CDRs from a murine antibody grafted into anon-human primate or human antibody V region framework, usually furthercomprising a human constant region, Riechmann et al., Nature 332(6162):323-7 (1988); Co et al., Nature 351(6326): 501-2 (1991); and U.S. Pat.Nos. 6,054,297; 5,821,337; 5,770,196; 5,766,886; 5,821,123; 5,869,619;6,180,377; 6,013,256; 5,693,761; and 6,180,370, the disclosures of whichare incorporated herein by reference in their entireties. Other usefulantibody derivatives of the invention include heteromeric antibodycomplexes and antibody fusions, such as diabodies (bispecificantibodies), single-chain diabodies, and intrabodies.

It is contemplated that the nucleic acids encoding the antibodies of thepresent invention can be operably joined to other nucleic acids forminga recombinant vector for cloning or for expression of the antibodies ofthe invention. Accordingly, the present invention includes anyrecombinant vector containing the coding sequences, or part thereof,whether for eukaryotic transduction, transfection or gene therapy. Suchvectors may be prepared using conventional molecular biology techniques,known to those with skill in the art, and would comprise DNA encodingsequences for the immunoglobulin V-regions including framework and CDRsor parts thereof, and a suitable promoter either with or without asignal sequence for intracellular transport Such vectors may betransduced or transfected into eukaryotic cells or used for gene therapy(Marasco et al., Proc. Natl. Acad. Sci. (USA) 90: 7889-7893 (1993); Duanet al., Proc. Natl. Acad. Sci. (USA) 91: 5075-5079 (1994), byconventional techniques, known to those with skill in the art.

The antibodies of the present invention, including fragments andderivatives thereof, can usefully be labeled. It is, therefore, anotheraspect of the present invention to provide labeled antibodies that bindspecifically to one or more of the polypeptides of the presentinvention, to one or more of the polypeptides encoded by the isolatednucleic acid molecules of the present invention, or the binding of whichcan be competitively inhibited by one or more of the polypeptides of thepresent invention or one or more of the polypeptides encoded by theisolated nucleic acid molecules of the present invention. The choice oflabel depends, in part, upon the desired use.

For example, when the antibodies of the present invention are used forimmunohistochemical staining of tissue samples, the label can usefullybe an enzyme that catalyzes production and local deposition of adetectable product. Enzymes typically conjugated to antibodies to permittheir immunohistochemical visualization are well known, and includealkaline phosphatase, β-galactosidase, glucose oxidase, horseradishperoxidase (HRP), and urease. Typical substrates for production anddeposition of visually detectable products includeo-nitrophenyl-beta-D-galactopyranoside (ONPG); o-phenylenediaminedihydrochloride (OPD); p-nitrophenyl phosphate (PNPP);p-nitrophenyl-beta-D-galactopyranoside PNPG); 3′,3′-diaminobenzidine(DAB); 3-amino-9-ethylcarbazole (AEC); 4-chloro-1-naphthol (CN);5-bromo-4-chloro-3-indolyl-phosphate (BCIP); ABTS®; BluoGal;iodonitrotetrazolium (INT); nitroblue tetrazolium chloride (NBT);phenazine methosulfate (PMS); phenolphthalein monophosphate (PMP);tetramethyl benzidine (TMB); tetranitroblue tetrazolium (TNBT); X-Gal;X-Gluc; and X-Glucoside.

Other substrates can be used to produce products for local depositionthat are luminescent. For example, in the presence of hydrogen peroxide(H₂O₂), horseradish peroxidase (HRP) can catalyze the oxidation ofcyclic diacylhydrazides, such as luminol. Immediately following theoxidation, the luminol is in an excited state (intermediate reactionproduct), which decays to the ground state by emitting light. Strongenhancement of the light emission is produced by enhancers, such asphenolic compounds. Advantages include high sensitivity, highresolution, and rapid detection without radioactivity and requiring onlysmall amounts of antibody. See, e.g., Thorpe et al., Methods Enzymol.133: 331-53 (1986); Kricka et al., J. Immunoassay 17(1): 67-83 (1996);and Lundqvist et al., J. Biolumin. Chemilumin. 10(6): 353-9 (1995). Kitsfor such enhanced chemiluminescent detection (ECL) are availablecommercially. The antibodies can also be labeled using colloidal gold.

As another example, when the antibodies of the present invention areused, e.g. for flow cytometric detection, for scanning laser cytometricdetection, or for fluorescent immunoassay, they can usefully be labeledwith fluorophores. There are a wide variety of fluorophore labels thatcan usefully be attached to the antibodies of the present invention. Forflow cytometric applications, both for extracellular detection and forintracellular detection, common useful fluorophores can be fluoresceinisothiocyanate (FITC), allophycocyanin (APC), R-phycoerytrin (PE),peridinin chlorophyll protein (PerCP), Texas Red, Cy3, Cy5, fluorescenceresonance energy tandem fluorophores such as PerCP-Cy5.5, PE-Cy5,PE-Cy5.5, PE-Cy7, PE-Texas Red, and APC-Cy7.

Other fluorophores include, inter alia, Alexa Fluor® 350, Alexa Fluor®488, Alexa Fluor® 532, Alexa Fluor® 546, Alexa Fluor® 568, Alexa Fluor®594, Alexa Fluor® 647 (monoclonal antibody labeling kits available fromMolecular Probes, Inc., Eugene, Oreg., USA), BODIPY dyes, such as BODIPY493/503, BODIPY FL, BODIPY R6G, BODIPY 530/550, BODIPY TMR, BODIPY558/568, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591,BODIPY TR, BODIPY 630/650, BODIPY 650/665, Cascade Blue, Cascade Yellow,Dansyl, lissamine rhodamine B, Marina Blue, Oregon Green 488, OregonGreen 514, Pacific Blue, rhodamine 6G, rhodamine green, rhodamine red,tetramethylrhodamine, Texas Red (available from Molecular Probes, Inc.,Eugene, Oreg., USA), and Cy2, Cy3, Cy3.5, Cy5, Cy5.5, Cy7, all of whichare also useful for fluorescently labeling the antibodies of the presentinvention. For secondary detection using labeled avidin, streptavidin,captavidin or neutravidin, the antibodies of the present invention canusefully be labeled with biotin.

When the antibodies of the present invention are used, e.g., for westernblotting applications, they can usefully be labeled with radioisotopes,such as ³³P, ³²P, ³⁵S, ³H, and ¹²⁵I. As another example, when theantibodies of the present invention are used for radioimmunotherapy, thelabel can usefully be ²²⁸Th, ²²⁷Ac, ²²⁵Ac, ²²³Ra, ²¹³Bi, ²¹²Pb, ²¹²Bi,²¹¹At, ²⁰³Pb, ¹⁹⁴Os, ¹⁸⁸Re, ¹⁸⁶Re, ¹⁵³Sm, ¹⁴⁹Tb, ¹³¹I, ¹²⁵I, ¹¹¹In,¹⁰⁵Rh, ^(99m)Tc, ⁹⁷Ru, ⁹⁰Y, ⁹⁰Sr, ⁸⁸Y, ⁷²Se, 67Cu, or ⁴⁷Sc.

As another example, when the antibodies of the present invention are tobe used for in vivo diagnostic use, they can be rendered detectable byconjugation to MRI contrast agents, such as gadoliniumdiethylenetriaminepentaacetic acid (DTPA), Lauffer et al., Radiology207(2): 529-38 (1998), or by radioisotopic labeling.

As would be understood, use of the labels described above is notrestricted to the application as for which they were mentioned.

The antibodies of the present invention, including fragments andderivatives thereof, can also be conjugated to toxins, in order totarget the toxin's ablative action to cells that display and/or expressthe polypeptides of the present invention. Commonly, the antibody insuch immunotoxins is conjugated to Pseudomonas exotoxin A, diphtheriatoxin, shiga toxin A, anthrax toxin lethal factor, or ricin. See Hall(ed.), Immunotoxin Methods and Protocols (Methods in Molecular Biology,vol. 166), Humana Press (2000); and Frankel et al. (eds.), ClinicalApplications of Immunotoxins, Springer-Verlag (1998).

The antibodies of the present invention can usefully be attached to asubstrate, and it is, therefore, another aspect of the invention toprovide antibodies that bind specifically to one or more of thepolypeptides of the present invention, to one or more of thepolypeptides encoded by the isolated nucleic acid molecules of thepresent invention, or the binding of which can be competitivelyinhibited by one or more of the polypeptides of the present invention orone or more of the polypeptides encoded by the isolated nucleic acidmolecules of the present invention, attached to a substrate. Substratescan be porous or nonporous, planar or nonplanar. For example, theantibodies of the present invention can usefully be conjugated tofiltration media, such as NHS-activated Sepharose or CNBr-activatedSepharose for purposes of immunoaffinity chromatography. For example,the antibodies of the present invention can usefully be attached toparamagnetic microspheres, typically by biotin-streptavidin interaction,which microsphere can then be used for isolation of cells that expressor display the polypeptides of the present invention. As anotherexample, the antibodies of the present invention can usefully beattached to the surface of a microtiter plate for ELISA.

As noted above, the antibodies of the present invention can be producedin prokaryotic and eukaryotic cells. It is, therefore, another aspect ofthe present invention to provide cells that express the antibodies ofthe present invention, including hybridoma cells, B cells, plasma cells,and host cells recombinantly modified to express the antibodies of thepresent invention.

In yet a further aspect, the present invention provides aptamers evolvedto bind specifically to one or more of the OSPs of the present inventionor to polypeptides encoded by the OSNAs of the invention.

In sum, one of skill in the art, provided with the teachings of thisinvention, has available a variety of methods which may be used to alterthe biological properties of the antibodies of this invention includingmethods which would increase or decrease the stability or half-life,immunogenicity, toxicity, affinity or yield of a given antibodymolecule, or to alter it in any other way that may render it moresuitable for a particular application.

Transgenic Animals and Cells

In another aspect, the invention provides transgenic cells and non-humanorganisms comprising nucleic acid molecules of the invention. In apreferred embodiment, the transgenic cells and non-human organismscomprise a nucleic acid molecule encoding an OSP. In a preferredembodiment, the OSP comprises an amino acid sequence selected from SEQID NO: 129-295, or a fragment, mutein, homologous protein or allelicvariant thereof. In another preferred embodiment, the transgenic cellsand non-human organism comprise an OSNA of the invention, preferably anOSNA comprising a nucleotide sequence selected from the group consistingof SEQ ID NO: 1-128, or a part, substantially similar nucleic acidmolecule, allelic variant or hybridizing nucleic acid molecule thereof.

In another embodiment, the transgenic cells and non-human organisms havea targeted disruption or replacement of the endogenous orthologue of thehuman OSG. The transgenic cells can be embryonic stem cells or somaticcells. The transgenic non-human organisms can be chimeric, nonchimericheterozygotes, and nonchimeric homozygotes. Methods of producingtransgenic animals are well known in the art. See, e.g. Hogan et al.,Manipulating the Mouse Embryo: A Laboratory Manual 2d ed., Cold SpringHarbor Press (1999); Jackson et al., Mouse Genetics and Transgenics: APractical Approach, Oxford University Press (2000); and Pinkert,Transgenic Animal Technology: A Laboratory Handbook, Academic Press(1999).

Any technique known in the art may be used to introduce a nucleic acidmolecule of the invention into an animal to produce the founder lines oftransgenic animals. Such techniques include, but are not limited to,pronuclear microinjection. (see, e.g., Paterson et al., Appl. Microbiol.Biotechnol. 40: 691-698 (1994); Carver et al., Biotechnology 11:1263-1270 (1993); Wright et al., Biotechnology 9: 830-834 (1991); andU.S. Pat. No. 4,873,191, herein incorporated by reference in itsentirety); retrovirus-mediated gene transfer into germ lines,blastocysts or embryos (see, e.g., Van der Putten et al., Proc. Natl.Acad. Sci., USA 82: 6148-6152 (1985)); gene targeting in embryonic stemcells (see, e.g., Thompson et al., Cell 56: 313-321 (1989));electroporation of cells or embryos (see, e.g., Lo, 1983, Mol. Cell.Biol. 3: 1803-1814 (1983)); introduction using a gene gun (see, e.g.,Ulmer et al., Science 259: 174549 (1993); introducing nucleic acidconstructs into embryonic pleuripotent stem cells and transferring thestem cells back into the blastocyst; and sperm-mediated gene transfer(see, e.g., Lavitrano et al., Cell 57: 717-723 (1989)).

Other techniques include, for example, nuclear transfer into enucleatedoocytes of nuclei from cultured embryonic, fetal, or adult cells inducedto quiescence (see, e.g., Campell et al., Nature 380: 64-66 (1996);Wilmut et al., Nature 385: 810-813 (1997)). The present inventionprovides for transgenic animals that carry the transgene (i.e., anucleic acid molecule of the invention) in all their cells, as well asanimals which carry the transgene in some, but not all their cells, i.e.e., mosaic animals or chimeric animals.

The transgene may be integrated as a single transgene or as multiplecopies, such as in concatamers, e.g., head-to-head tandems orhead-to-tail tandems. The transgene may also be selectively introducedinto and activated in a particular cell type by following, e.g., theteaching of Lasko et al. et al., Proc. Natl. Acad. Sci. USA 89:6232-6236 (1992). The regulatory sequences required for such a cell-typespecific activation will depend upon the particular cell type ofinterest, and will be apparent to those of skill in the art.

Once transgenic animals have been generated, the expression of therecombinant gene may be assayed utilizing standard techniques. Initialscreening may be accomplished by Southern blot analysis or PCRtechniques to analyze animal tissues to verify that integration of thetransgene has taken place. The level of mRNA expression of the transgenein the tissues of the transgenic animals may also be assessed usingtechniques which include, but are not limited to, Northern blot analysisof tissue samples obtained from the animal, in situ hybridizationanalysis, and reverse transcriptase-PCR (RT-PCR). Samples of transgenicgene-expressing tissue may also be evaluated immunocytochemically orimmunohistochemically using antibodies specific for the transgeneproduct

Once the founder animals are produced, they may be bred, inbred,outbred, or crossbred to produce colonies of the particular animal.Examples of such breeding strategies include, but are not limited to:outbreeding of founder animals with more than one integration site inorder to establish separate lines; inbreeding of separate lines in orderto produce compound transgenics that express the transgene at higherlevels because of the effects of additive expression of each transgene;crossing of heterozygous transgenic animals to produce animalshomozygous for a given integration site in order to both augmentexpression and eliminate the need for screening of animals by DNAanalysis; crossing of separate homozygous lines to produce compoundheterozygous or homozygous lines; and breeding to place the transgene ona distinct background that is appropriate for an experimental model ofinterest.

Transgenic animals of the invention have uses which include, but are notlimited to, animal model systems useful in elaborating the biologicalfunction of polypeptides of the present invention, studying conditionsand/or disorders associated with aberrant expression, and in screeningfor compounds effective in ameliorating such conditions and/ordisorders.

Methods for creating a transgenic animal with a disruption of a targetedgene are also well known in the art. In general, a vector is designed tocomprise some nucleotide sequences homologous to the endogenous targetedgene. The vector is introduced into a cell so that it may integrate, viahomologous recombination with chromosomal sequences, into the endogenousgene, thereby disrupting the function of the endogenous gene. Thetransgene may also be selectively introduced into a particular celltype, thus inactivating the endogenous gene in only that cell type. See,e.g., Gu et al, Science 265: 103-106 (1994). The regulatory sequencesrequired for such a cell-type specific inactivation will depend upon theparticular cell type of interest, and will be apparent to those of skillin the art. See, e.g., Smithies et al., Nature 317: 230-234 (1985);Thomas et al., Cell 51: 503-512 (1987); Thompson et al., Cell 5: 313-321(1989).

In one embodiment, a mutant, non-functional nucleic acid molecule of theinvention (or a completely unrelated DNA sequence) flanked by DNAhomologous to the endogenous nucleic acid sequence (either the codingregions or regulatory regions of the gene) can be used, with or withouta selectable marker and/or a negative selectable marker, to transfectcells that express polypeptides of the invention in vivo. In anotherembodiment, techniques known in the art are used to generate knockoutsin cells that contain, but do not express the gene of interest Insertionof the DNA construct, via targeted homologous recombination, results ininactivation of the targeted gene. Such approaches are particularlysuited in research and agricultural fields where modifications toembryonic stem cells can be used to generate animal offspring with aninactive targeted gene. See, e.g., Thomas, supra and Thompson, supra.However this approach can be routinely adapted for use in humansprovided the recombinant DNA constructs are directly administered ortargeted to the required site in vivo using appropriate viral vectorsthat will be apparent to those of skill in the art.

In further embodiments of the invention, cells that are geneticallyengineered to express the polypeptides of the invention, oralternatively, that are genetically engineered not to express thepolypeptides of the invention (e.g., knockouts) are administered to apatient in vivo. Such cells may be obtained from an animal or patient oran MHC compatible donor and can include, but are not limited tofibroblasts, bone marrow cells, blood cells (e.g., lymphocytes),adipocytes, muscle cells, endothelial cells etc. The cells aregenetically engineered in vitro using recombinant DNA techniques tointroduce the coding sequence of polypeptides of the invention into thecells, or alternatively, to disrupt the coding sequence and/orendogenous regulatory sequence associated with the polypeptides of theinvention, e.g., by transduction (using viral vectors, and preferablyvectors that integrate the transgene into the cell genome) ortransfection procedures, including, but not limited to, the use ofplasmids, cosmids, YACs, naked DNA, electroporation, liposomes, etc.

The coding sequence of the polypeptides of the invention can be placedunder the control of a strong constitutive or inducible promoter orpromoter/enhancer to achieve expression, and preferably secretion, ofthe polypeptides of the invention. The engineered cells which expressand preferably secrete the polypeptides of the invention can beintroduced into the patient systemically, e.g., in the circulation, orintraperitoneally.

Alternatively, the cells can be incorporated into a matrix and implantedin the body, e.g., genetically engineered fibroblasts can be implantedas part of a skin graft; genetically engineered endothelial cells can beimplanted as part of a lymphatic or vascular graft. See, e.g., U.S. Pat.Nos. 5,399,349 and 5,460,959, each of which is incorporated by referenceherein in its entirety.

When the cells to be administered are non-autologous or non-MHCcompatible cells, they can be administered using well known techniqueswhich prevent the development of a host immune response against theintroduced cells. For example, the cells may be introduced in anencapsulated form which, while allowing for an exchange of componentswith the immediate extracellular environment, does not allow theintroduced cells to be recognized by the host immune system.

Transgenic and “knock-out” animals of the invention have uses whichinclude, but are not limited to, animal model systems useful inelaborating the biological function of polypeptides of the presentinvention, studying conditions and/or disorders associated with aberrantexpression, and in screening for compounds effective in amelioratingsuch conditions and/or disorders.

Computer Readable Means

A further aspect of the invention is a computer readable means forstoring the nucleic acid and amino acid sequences of the instantinvention. In a preferred embodiment, the invention provides a computerreadable means for storing SEQ ID NO: 129-295 and SEQ ID NO: 1-128 asdescribed herein, as the complete set of sequences or in anycombination. The records of the computer readable means can be accessedfor reading and display and for interface with a computer system for theapplication of programs allowing for the location of data upon a queryfor data meeting certain criteria, the comparison of sequences, thealignment or ordering of sequences meeting a set of criteria, and thelike.

The nucleic acid and amino acid sequences of the invention areparticularly useful as components in databases useful for searchanalyses as well as in sequence analysis algorithms. As used herein, theterms “nucleic acid sequences of the invention” and “amino acidsequences of the invention” mean any detectable chemical or physicalcharacteristic of a polynucleotide or polypeptide of the invention thatis or may be reduced to or stored in a computer readable form. Theseinclude, without limitation, chromatographic scan data or peak data,photographic data or scan data therefrom, and mass spectrographic data.

This invention provides computer readable media having stored thereonsequences of the invention. A computer readable medium may comprise oneor more of the following: a nucleic acid sequence comprising a sequenceof a nucleic acid sequence of the invention; an amino acid sequencecomprising an amino acid sequence of the invention; a set of nucleicacid sequences wherein at least one of said sequences comprises thesequence of a nucleic acid sequence of the invention; a set of aminoacid sequences wherein at least one of said sequences comprises thesequence of an amino acid sequence of the invention; a data setrepresenting a nucleic acid sequence comprising the sequence of one ormore nucleic acid sequences of the invention; a data set representing anucleic acid sequence encoding an amino acid sequence comprising thesequence of an amino acid sequence of the invention; a set of nucleicacid sequences wherein at least one of said sequences comprises thesequence of a nucleic acid sequence of the invention; a set of aminoacid sequences wherein at least one of said sequences comprises thesequence of an amino acid sequence of the invention; a data setrepresenting a nucleic acid sequence comprising the sequence of anucleic acid sequence of the invention; a data set representing anucleic acid sequence encoding an amino acid sequence comprising thesequence of an amino acid sequence of the invention. The computerreadable medium can be any composition of matter used to storeinformation or data, including, for example, commercially availablefloppy disks, tapes, hard drives, compact disks, and video disks.

Also provided by the invention are methods for the analysis of charactersequences, particularly genetic sequences. Preferred methods of sequenceanalysis include, for example, methods of sequence homology analysis,such as identity and similarity analysis, RNA structure analysis,sequence assembly, cladistic analysis, sequence motif analysis, openreading frame determination, nucleic acid base calling, and sequencingchromatogram peak analysis.

A computer-based method is provided for performing nucleic acid sequenceidentity or similarity identification. This method comprises the stepsof providing a nucleic acid sequence comprising the sequence of anucleic acid of the invention in a computer readable medium; andcomparing said nucleic acid sequence to at least one nucleic acid oramino acid sequence to identify sequence identity or similarity.

A computer-based method is also provided for performing amino acidhomology identification, said method comprising the steps of: providingan amino acid sequence comprising the sequence of an amino acid of theinvention in a computer readable medium; and comparing said amino acidsequence to at least one nucleic acid or an amino acid sequence toidentify homology.

A computer-based method is still further provided for assembly ofoverlapping nucleic acid sequences into a single nucleic acid sequence,said method comprising the steps of: providing a first nucleic acidsequence comprising the sequence of a nucleic acid of the invention in acomputer readable medium; and screening for at least one overlappingregion between said first nucleic acid sequence and a second nucleicacid sequence. In addition, the invention includes a method of usingpatterns of expression associated with either the nucleic acids orproteins in a computer-based method to diagnose disease.

Diagnostic Methods for Ovarian Cancer

The present invention also relates to quantitative and qualitativediagnostic assays and methods for detecting, diagnosing, monitoring,staging and predicting cancers by comparing expression of an OSNA or anOSP in a human patient that has or may have ovarian cancer, or who is atrisk of developing ovarian cancer, with the expression of an OSNA or anOSP in a normal human control. For purposes of the present invention,“expression of an OSNA” or “OSNA expression” means the quantity of OSNAmRNA that can be measured by any method known in the art or the level oftranscription that can be measured by any method known in the art in acell, tissue, organ or whole patient. Similarly, the term “expression ofan OSP” or “OSP expression” means the amount of OSP that can be measuredby any method known in the art or the level of translation of an OSNAthat can be measured by any method known in the art.

The present invention provides methods for diagnosing ovarian cancer ina patient, by analyzing for changes in levels of OSNA or OSP in cells,tissues, organs or bodily fluids compared with levels of OSNA or OSP incells, tissues, organs or bodily fluids of preferably the same type froma normal human control, wherein an increase, or decrease in certaincases, in levels of an OSNA or OSP in the patient versus the normalhuman control is associated with the presence of ovarian cancer or witha predilection to the disease. In another preferred embodiment, thepresent invention provides methods for diagnosing ovarian cancer in apatient by analyzing changes in the structure of the mRNA of an OSGcompared to the mRNA from a normal control. These changes include,without limitation, aberrant splicing, alterations in polyadenylationand/or alterations in 5′ nucleotide capping. In yet another preferredembodiment, the present invention provides methods for diagnosingovarian cancer in a patient by analyzing changes in an OSP compared toan OSP from a normal patient. These changes include, e.g., alterations,including post translational modifications such as glycosylation and/orphosphorylation of the OSP or changes in the subcellular OSPlocalization.

For purposes of the present invention, diagnosing means that OSNA or OSPlevels are used to determine the presence or absence of disease in apatient. As will be understood by those of skill in the art, measurementof other diagnostic parameters may be required for definitive diagnosisor determination of the appropriate treatment for the disease. Thedetermination may be made by a clinician, a doctor, a testinglaboratory, or a patient using an over the counter test. The patient mayhave symptoms of disease or may be asymptomatic. In addition, the OSNAor OSP levels of the present invention may be used as screening markerto determine whether further tests or biopsies are warranted. Inaddition, the OSNA or OSP levels may be used to determine thevulnerability or susceptibility to disease.

In a preferred embodiment, the expression of an OSNA is measured bydetermining the amount of a mRNA that encodes an amino acid sequenceselected from SEQ ID NO: 129-295, a homolog, an allelic variant, or afragment thereof. In a more preferred embodiment, the OSNA expressionthat is measured is the level of expression of an OSNA mRNA selectedfrom SEQ ID NO: 1-128, or a hybridizing nucleic acid, homologous nucleicacid or allelic variant thereof, or a part of any of these nucleic acidmolecules. OSNA expression may be measured by any method known in theart, such as those described supra, including measuring mRNA expressionby Northern blot, quantitative or qualitative reverse transcriptase PCR(RT-PCR), microarray, dot or slot blots or in situ hybridization. See,e.g., Ausubel (1992), supra; Ausubel (1999), Supra; Sambrook (1989),supra; and Sambrook (2001), supra. OSNA transcription may be measured byany method known in the art including using a reporter gene hooked up tothe promoter of an OSG of interest or doing nuclear run-off assays.Alterations in mRNA structure, e.g., aberrant splicing variants, may bedetermined by any method known in the art, including, RT-PCR followed bysequencing or restriction analysis. As necessary, OSNA expression may becompared to a known control such as normal ovarian nucleic acid, todetect a change in expression.

In another preferred embodiment, the expression of an OSP is measured bydetermining the level of an OSP having an amino acid sequence selectedfrom the group consisting of SEQ ID NO: 129-295, a homolog, an allelicvariant, or a fragment thereof. Such levels are preferably determined inat least one of cells, tissues, organs and/or bodily fluids, includingdetermination of normal and abnormal levels. Thus, for instance, adiagnostic assay in accordance with the invention for diagnosing over-or underexpression of an OSNA or OSP compared to normal control bodilyfluids, cells, or tissue samples may be used to diagnose the presence ofovarian cancer. The expression level of an OSP may be determined by anymethod known in the art, such as those described supra. In a preferredembodiment, the OSP expression level may be determined byradioimmunoassays, competitive-binding assays, ELISA, Western blot,FACS, immunohistochemistry, immunoprecipitation, proteomic approaches:two-dimensional gel electrophoresis (2D electrophoresis) andnon-gel-based approaches such as mass spectrometry or proteininteraction profiling. See, e.g., Harlow (1999), supra; Ausubel (1992),supra; and Ausubel (1999), supra. Alterations in the OSP structure maybe determined by any method known in the art, including, e.g. usingantibodies that specifically recognize phosphoserine, phosphothreonineor phosphotyrosine residues, two-dimensional polyacrylamide gelelectrophoresis (2D PAGE) and/or chemical analysis of amino acidresidues of the protein. Id.

In a preferred embodiment, a radioimmunoassay (RIA) or an ELISA is used.An antibody specific to an OSP is prepared if one is not alreadyavailable. In a preferred embodiment, the antibody is a monoclonalantibody. The anti-OSP antibody is bound to a solid support and any freeprotein binding sites on the solid support are blocked with a proteinsuch as bovine serum albumin. A sample of interest is incubated with theantibody on the solid support under conditions in which the OSP willbind to the anti-OSP antibody. The sample is removed, the solid supportis washed to remove unbound material, and an anti-OSP antibody that islinked to a detectable reagent (a radioactive substance for RIA and anenzyme for ELISA) is added to the solid support and incubated underconditions in which binding of the OSP to the labeled antibody willoccur. After binding, the unbound labeled antibody is removed bywashing. For an ELISA, one or more substrates are added to produce acolored reaction product that is based upon the amount of an OSP in thesample. For an RIA, the solid support is counted for radioactive decaysignals by any method known in the art. Quantitative results for bothRIA and ELISA typically are obtained by reference to a standard curve.

Other methods to measure OSP levels are known in the art. For instance,a competition assay may be employed wherein an anti-OSP antibody isattached to a solid support and an allocated amount of a labeled OSP anda sample of interest are incubated with the solid support. The amount oflabeled OSP attached to the solid support can be correlated to thequantity of an OSP in the sample.

Of the proteomic approaches, 2D PAGE is a well known technique.Isolation of individual proteins from a sample such as serum isaccomplished using sequential separation of proteins by isoelectricpoint and molecular weight. Typically, polypeptides are first separatedby isoelectric point (the first dimension) and then separated by sizeusing an electric current (the second dimension). In general, the seconddimension is perpendicular to the first dimension. Because no twoproteins with different sequences are identical on the basis of bothsize and charge, the result of 2D PAGE is a roughly square gel in whicheach protein occupies a unique spot. Analysis of the spots with chemicalor antibody probes, or subsequent protein microsequencing can reveal therelative abundance of a given protein and the identity of the proteinsin the sample.

Expression levels of an OSNA can be determined by any method known inthe art, including PCR and other nucleic acid methods, such as ligasechain reaction (LCR) and nucleic acid sequence based amplification(NASBA), can be used to detect malignant cells for diagnosis andmonitoring of various malignancies. For example, reverse-transcriptasePCR (RT-PCR) is a powerful technique which can be used to detect thepresence of a specific mRNA population in a complex mixture of thousandsof other mRNA species. In RT-PCR, an mRNA species is first reversetranscribed to complementary DNA (cDNA) with use of the enzyme reversetranscriptase; the cDNA is then amplified as in a standard PCR reaction.

Hybridization to specific DNA molecules (e.g., oligonucleotides) arrayedon a solid support can be used to both detect the expression of andquantitate the level of expression of one or more OSNAs of interest. Inthis approach, all or a portion of one or more OSNAs is fixed to asubstrate. A sample of interest, which may comprise RNA, e.g., total RNAor polyA-selected mRNA, or a complementary DNA (cDNA) copy of the RNA isincubated with the solid support under conditions in which hybridizationwill occur between the DNA on the solid support and the nucleic acidmolecules in the sample of interest. Hybridization between thesubstrate-bound DNA and the nucleic acid molecules in the sample can bedetected and quantitated by several means, including, withoutlimitation, radioactive labeling or fluorescent labeling of the nucleicacid molecule or a secondary molecule designed to detect the hybrid.

The above tests can be carried out on samples derived from a variety ofcells, bodily fluids and/or tissue extracts such as homogenates orsolubilized tissue obtained from a patient. Tissue extracts are obtainedroutinely from tissue biopsy and autopsy material. Bodily fluids usefulin the present invention include blood, urine, saliva or any otherbodily secretion or derivative thereof. As used herein “blood” includeswhole blood, plasma, serum, circulating epithelial cells, constituents,or any derivative of blood.

In addition to detection in bodily fluids, the proteins and nucleicacids of the invention are suitable to detection by cell capturetechnology. Whole cells may be captured by a variety methods for examplemagnetic separation, such as described in U.S. Pat. Nos. 5,200,084;5,186,827; 5,108,933; and 4,925,788, the disclosures of which areincorporated herein by reference in their entireties. Epithelial cellsmay be captured using such products as Dynabeads® or CELLection™ (DynalBiotech, Oslo, Norway). Alternatively, fractions of blood may becaptured, e.g., the buffy coat fraction (50 mm cells isolated from 5 mlof blood) containing epithelial cells. In addition, cancer cells may becaptured using the techniques described in WO 00/47998, the disclosureof which is incorporated herein by reference in its entirety. Once thecells are captured or concentrated, the proteins or nucleic acids aredetected by the means described in the subject application.Alternatively, nucleic acids may be captured directly from bloodsamples, see U.S. Pat. Nos. 6,156,504, 5,501,963; or WO 01/42504, thedisclosures of which are incorporated herein by reference in theirentireties.

In a preferred embodiment the specimen tested for expression of OSNA orOSP includes without limitation ovarian tissue, ovarian cells grown incell culture, blood, serum, lymph node tissue, and lymphatic fluid. Inanother preferred embodiment, especially when metastasis of a primaryovarian cancer is known or suspected, specimens include, withoutlimitation, tissues from brain, bone, bone marrow, liver, lungs, colon,and adrenal glands. In general, the tissues may be sampled by biopsy,including, without limitation, needle biopsy, e.g., taansthoracic needleaspiration, cervical mediatinoscopy, endoscopic lymph node biopsy,video-assisted thoracoscopy, exploratory thoracotomy, bone marrow biopsyand bone marrow aspiration.

All the methods of the present invention may optionally includedetermining the expression levels of one or more other cancer markers inaddition to determining the expression level of an OSNA or OSP. In manycases, the use of another cancer marker will decrease the likelihood offalse positives or false negatives. In one embodiment, the one or moreother cancer markers include other OSNAs or OSPs as disclosed herein.Other cancer markers useful in the present invention will depend on thecancer being tested and are known to those of skill in the art. In apreferred embodiment, at least one other cancer marker in addition to aparticular OSNA or OSP is measured. In a more preferred embodiment, atleast two other additional cancer markers are used. In an even morepreferred embodiment, at least three, more preferably at least five,even more preferably at least ten additional cancer markers are used.

Diagnosing

In one aspect, the invention provides a method for determining theexpression levels and/or structural alterations of one or more OSNAand/or OSP in a sample from a patient suspected of having ovariancancer. In general, the method comprises the steps of obtaining thesample from the patient, determining the expression level or structuralalterations of an OSNA and/or OSP and then ascertaining whether thepatient has ovarian cancer from the expression level of the OSNA or OSP.In general, if high expression relative to a control of an OSNA or OSPis indicative of ovarian cancer, a diagnostic assay is consideredpositive if the level of expression of the OSNA or OSP is at least oneand a half times higher, and more preferably are at least two timeshigher, still more preferably five times higher, even more preferably atleast ten times higher, than in preferably the same cells, tissues orbodily fluid of a normal human control. In contrast, if low expressionrelative to a control of an OSNA or OSP is indicative of ovarian cancer,a diagnostic assay is considered positive if the level of expression ofthe OSNA or OSP is at least one and a half times lower, and morepreferably are at least two times lower, still more preferably fivetimes lower, even more preferably at least ten times lower than inpreferably the same cells, tissues or bodily fluid of a normal humancontrol. The normal human control may be from a different patient orfrom uninvolved tissue of the same patient.

The present invention also provides a method of determining whetherovarian cancer has metastasized in a patient One may identify whetherthe ovarian cancer has metastasized by measuring the expression levelsand/or structural alterations of one or more OSNAs and/or OSPs in avariety of tissues. The presence of an OSNA or OSP in a tissue otherthan ovarian at levels higher than that of corresponding noncanceroustissue (e.g., the same tissue from another individual) is indicative ofmetastasis if high level expression of an OSNA or OSP is associated withovarian cancer. Similarly, the presence of an OSNA or OSP in a tissueother than ovarian at levels lower than that of correspondingnoncancerous tissue is indicative of metastasis if low level expressionof an OSNA or OSP is associated with ovarian cancer. Further, thepresence of a structurally altered OSNA or OSP that is associated withovarian cancer is also indicative of metastasis.

In general, if high expression relative to a control of an OSNA or OSPis indicative of metastasis, an assay for metastasis is consideredpositive if the level of expression of the OSNA or OSP is at least oneand a half times higher, and more preferably are at least two timeshigher, still more preferably five times higher, even more preferably atleast ten times higher, than in preferably the same cells, tissues orbodily fluid of a normal human control. In contrast, if low expressionrelative to a control of an OSNA or OSP is indicative of metastasis, anassay for metastasis is considered positive if the level of expressionof the OSNA or OSP is at least one and a half times lower, and morepreferably are at least two times lower, still more preferably fivetimes lower, even more preferably at least ten times lower than inpreferably the same cells, tissues or bodily fluid of a normal humancontrol.

Staging

The invention also provides a method of staging ovarian cancer in ahuman patient. The method comprises identifying a human patient havingovarian cancer and analyzing cells, tissues or bodily fluids from suchhuman patient for expression levels and/or structural alterations of oneor more OSNAs or OSPs. First, one or more tumors from a variety ofpatients are staged according to procedures well known in the art, andthe expression levels of one or more OSNAs or OSPs is determined foreach stage to obtain a standard expression level for each OSNA and OSP.Then, the OSNA or OSP expression levels of the OSNA or OSP aredetermined in a biological sample from a patient whose stage of canceris not known. The OSNA or OSP expression levels from the patient arethen compared to the standard expression level. By comparing theexpression level of the OSNAs and OSPs from the patient to the standardexpression levels, one may determine the stage of the tumor. The sameprocedure may be followed using structural alterations of an OSNA or OSPto determine the stage of a ovarian cancer.

Monitoring

Further provided is a method of monitoring ovarian cancer in a humanpatient One may monitor a human patient to determine whether there hasbeen metastasis and, if there has been, when metastasis began to occur.One may also monitor a human patient to determine whether apreneoplastic lesion has become cancerous. One may also monitor a humanpatient to determine whether a therapy, e.g., chemotherapy, radiotherapyor surgery, has decreased or eliminated the ovarian cancer. Themonitoring may determine if there has been a reoccurrence and, if so,determine its nature. The method comprises identifying a human patientthat one wants to monitor for ovarian cancer, periodically analyzingcells, tissues or bodily fluids from such human patient for expressionlevels of one or more OSNAs or OSPs, and comparing the OSNA or OSPlevels over time to those OSNA or OSP expression levels obtainedpreviously. Patients may also be monitored by measuring one or morestructural alterations in an OSNA or OSP that are associated withovarian cancer.

If increased expression of an OSNA or OSP is associated with metastasis,treatment failure, or conversion of a preneoplastic lesion to acancerous lesion, then detecting an increase in the expression level ofan OSNA or OSP indicates that the tumor is metastasizing, that treatmenthas failed or that the lesion is cancerous, respectively. One havingordinary skill in the art would recognize that if this were the case,then a decreased expression level would be indicative of no metastasis,effective therapy or failure to progress to a neoplastic lesion. Ifdecreased expression of an OSNA or OSP is associated with metastasis,treatment failure, or conversion of a preneoplastic lesion to acancerous lesion, then detecting a decrease in the expression level ofan OSNA or OSP indicates that the tumor is metastasizing, that treatmenthas failed or that the lesion is cancerous, respectively. In a preferredembodiment, the levels of OSNAs or OSPs are determined from the samecell type, tissue or bodily fluid as prior patient samples. Monitoring apatient for onset of ovarian cancer metastasis is periodic andpreferably is done on a quarterly basis, but may be done more or lessfrequently.

The methods described herein can further be utilized as prognosticassays to identify subjects having or at risk of developing a disease ordisorder associated with increased or decreased expression levels of anOSNA and/or OSP. The present invention provides a method in which a testsample is obtained from a human patient and one or more OSNAs and/orOSPs are detected. The presence of higher (or lower) OSNA or OSP levelsas compared to normal human controls is diagnostic for the human patientbeing at risk for developing cancer, particularly ovarian cancer. Theeffectiveness of therapeutic agents to decrease (or increase) expressionor activity of one or more OSNAs and/or OSPs of the invention can alsobe monitored by analyzing levels of expression of the OSNAs and/or OSPsin a human patient in clinical trials or in in vitro screening assayssuch as in human cells. In this way, the gene expression pattern canserve as a marker, indicative of the physiological response of the humanpatient or cells, as the case may be, to the agent being tested.

Detection of Genetic Lesions or Mutations

The methods of the present invention can also be used to detect geneticlesions or mutations in an OSG, thereby determining if a human with thegenetic lesion is susceptible to developing ovarian cancer or todetermine what genetic lesions are responsible, or are partlyresponsible, for a person's existing ovarian cancer. Genetic lesions canbe detected, for example, by ascertaining the existence of a deletion,insertion and/or substitution of one or more nucleotides from the OSGsof this invention, a chromosomal rearrangement of an OSG, an aberrantmodification of an OSG (such as of the methylation pattern of thegenomic DNA), or allelic loss of an OSG. Methods to detect such lesionsin the OSG of this invention are known to those having ordinary skill inthe art following the teachings of the specification.

Methods of Detecting Noncancerous Ovarian Diseases

The present invention also provides methods for determining theexpression levels and/or structural alterations of one or more OSNAsand/or OSPs in a sample from a patient suspected of having or known tohave a noncancerous ovarian disease. In general, the method comprisesthe steps of obtaining a sample from the patient, determining theexpression level or structural alterations of an OSNA and/or OSP,comparing the expression level or structural alteration of the OSNA orOSP to a normal ovarian control, and then ascertaining whether thepatient has a noncancerous ovarian disease. In general, if highexpression relative to a control of an OSNA or OSP is indicative of aparticular noncancerous ovarian disease, a diagnostic assay isconsidered positive if the level of expression of the OSNA or OSP is atleast two times higher, and more preferably are at least five timeshigher, even more preferably at least ten times higher, than inpreferably the same cells, tissues or bodily fluid of a normal humancontrol. In contrast, if low expression relative to a control of an OSNAor OSP is indicative of a noncancerous ovarian disease, a diagnosticassay is considered positive if the level of expression of the OSNA orOSP is at least two times lower, more preferably are at least five timeslower, even more preferably at least ten times lower than in preferablythe same cells, tissues or bodily fluid of a normal human control. Thenormal human control may be from a different patient or from uninvolvedtissue of the same patient.

One having ordinary skill in the art may determine whether an OSNAand/or OSP is associated with a particular noncancerous ovarian diseaseby obtaining ovarian tissue from a patient having a noncancerous ovariandisease of interest and determining which OSNAs and/or OSPs areexpressed in the tissue at either a higher or a lower level than innormal ovarian tissue. In another embodiment, one may determine whetheran OSNA or OSP exhibits structural alterations in a particularnoncancerous ovarian disease state by obtaining ovarian tissue from apatient having a noncancerous ovarian disease of interest anddetermining the structural alterations in one or more OSNAs and/or OSPsrelative to normal ovarian tissue.

Methods for Identifying Ovarian Tissue

In another aspect, the invention provides methods for identifyingovarian tissue. These methods are particularly useful in, e.g., forensicscience, ovarian cell differentiation and development, and in tissueengineering.

In one embodiment, the invention provides a method for determiningwhether a sample is ovarian tissue or has ovarian tissue-likecharacteristics. The method comprises the steps of providing a samplesuspected of comprising ovarian tissue or having ovarian tissue-likecharacteristics, determining whether the sample expresses one or moreOSNAs and/or OSPs, and, if the sample expresses one or more OSNAs and/orOSPs, concluding that the sample comprises ovarian tissue. In apreferred embodiment, the OSNA encodes a polypeptide having an aminoacid sequence selected from SEQ ID NO: 129-295, or a homolog, allelicvariant or fragment thereof. In a more preferred embodiment, the OSNAhas a nucleotide sequence selected from SEQ ID NO: 1-128, or ahybridizing nucleic acid, an allelic variant or a part thereof.Determining whether a sample expresses an OSNA can be accomplished byany method known in the art. Preferred methods include hybridization tomicroarrays, Northern blot hybridization, and quantitative orqualitative RT-PCR. In another preferred embodiment, the method can bepracticed by determining whether an OSP is expressed. Determiningwhether a sample expresses an OSP can be accomplished by any methodknown in the art. Preferred methods include Western blot, ELISA, RIA and2D PAGE. In one embodiment, the OSP has an amino acid sequence selectedfrom SEQ ID NO: 129-295, or a homolog, allelic variant or fragmentthereof In another preferred embodiment, the expression of at least twoOSNAs and/or OSPs is determined. In a more preferred embodiment, theexpression of at least three, more preferably four and even morepreferably five OSNAs and/or OSPs are determined.

In one embodiment, the method can be used to determine whether anunknown tissue is ovarian tissue. This is particularly useful inforensic science, in which small, damaged pieces of tissues that are notidentifiable by microscopic or other means are recovered from a crime oraccident scene. In another embodiment, the method can be used todetermine whether a tissue is differentiating or developing into ovariantissue. This is important in monitoring the effects of the addition ofvarious agents to cell or tissue culture, e.g., in producing new ovariantissue by tissue engineering. These agents include, e.g., growth anddifferentiation factors, extracellular matrix proteins and culturemedium. Other factors that may be measured for effects on tissuedevelopment and differentiation include gene transfer into the cells ortissues, alterations in pH, aqueous:air interface and various otherculture conditions.

Methods for Producing and Modifying Ovarian Tissue

In another aspect, the invention provides methods for producingengineered ovarian tissue or cells. In one embodiment, the methodcomprises the steps of providing cells, introducing an OSNA or an OSGinto the cells, and growing the cells under conditions in which theyexhibit one or more properties of ovarian tissue cells. In a preferredembodiment, the cells are pleuripotent. As is well known in the art,normal ovarian tissue comprises a large number of different cell types.Thus, in one embodiment, the engineered ovarian tissue or cellscomprises one of these cell types. In another embodiment, the engineeredovarian tissue or cells comprises more than one ovarian cell type.Further, the culture conditions of the cells or tissue may requiremanipulation in order to achieve full differentiation and development ofthe ovarian cell tissue. Methods for manipulating culture conditions arewell known in the art.

Nucleic acid molecules encoding one or more OSPs are introduced intocells, preferably pleuripotent cells. In a preferred embodiment, thenucleic acid molecules encode OSPs having amino acid sequences selectedfrom SEQ ID NO: 129-295, or homologous proteins, analogs, allelicvariants or fragments thereof. In a more preferred embodiment, thenucleic acid molecules have a nucleotide sequence selected from SEQ IDNO: 1-128, or hybridizing nucleic acids, allelic variants or partsthereof. In another highly preferred embodiment, an OSG is introducedinto the cells. Expression vectors and methods of introducing nucleicacid molecules into cells are well known in the art and are described indetail, supra.

Artificial ovarian tissue may be used to treat patients who have lostsome or all of their ovarian function.

Pharmaceutical Compositions

In another aspect, the invention provides pharmaceutical compositionscomprising the nucleic acid molecules, polypeptides, fusion proteins,antibodies, antibody derivatives, antibody fragments, agonists,antagonists, or inhibitors of the present invention. In a preferredembodiment, the pharmaceutical composition comprises an OSNA or partthereof. In a more preferred embodiment, the OSNA has a nucleotidesequence selected from the group consisting of SEQ ID NO: 1-128, anucleic acid that hybridizes thereto, an allelic variant thereof, or anucleic acid that has substantial sequence identity thereto. In anotherpreferred embodiment, the pharmaceutical composition comprises an OSP orfragment thereof. In a more preferred embodiment, the pharmaceuticalcomposition comprises an OSP having an amino acid sequence that isselected from the group consisting of SEQ ID NO: 129-295, a polypeptidethat is homologous thereto, a fusion protein comprising all or a portionof the polypeptide, or an analog or derivative thereof. In anotherpreferred embodiment, the pharmaceutical composition comprises ananti-OSP antibody, preferably an antibody that specifically binds to anOSP having an amino acid that is selected from the group consisting ofSEQ ID NO: 129-295, or an antibody that binds to a polypeptide that ishomologous thereto, a fusion protein comprising all or a portion of thepolypeptide, or an analog or derivative thereof.

Due to the association of angiogenesis with cancer vascularization thereis great need of new markers and methods for diagnosing angiogenesisactivity to identify developing tumors and angiogenesis relateddiseases. Furthermore, great need is also present for new moleculartargets useful in the treatment of angiogenesis and angiogenesis relateddiseases such as cancer. In addition known modulators of angiogenesissuch as endostatin or vascular endothelial growth factor (VEGF). Use ofthe methods and compositions disclosed herein in combination withanti-angiogenesis drugs, drugs that block the matrix breakdown (such asBMS-275291, Dalteparin (Fragmin®), Suramin), drugs that inhibitendothelial cells (2-methoxyestradiol (2-ME), CC-5013 (ThalidomideAnalog), Combretastatin A4 Phosphate, LY317615 (Protein Kinase C BetaInhibitor), Soy Isoflavone (Genistein; Soy Protein Isolate),Thalidomide), drugs that block activators of angiogenesis (AE-941(Neovastat™; GW786034), Anti-VEGF Antibody (Bevacizumab; Avastin™),Interferon-alpha, PTK787/ZK 222584, VEGF-Trap, ZD6474), Drugs thatinhibit endothelial-specific integrin/survival signaling (EMD 121974,Anti-Anb3 Integrin Antibody (Medi-522; Vitaxin™)).

Such a composition typically contains from about 0.1 to 90% by weight ofa therapeutic agent of the invention formulated in and/or with apharmaceutically acceptable carrier or excipient.

Pharmaceutical formulation is a well-established art that is furtherdescribed in Gennaro (ed.), Remington: The Science and Practice ofPharmacy, 20^(th) ed., Lippincott, Williams & Wilkins (2000); Ansel etal., Pharmaceutical Dosage Forms and Drug Delivery Systems, 7^(th) ed.,Lippincott Williams & Wilkins (1999); and Kibbe (ed.), Handbook ofPharmaceutical Excipients American Pharmaceutical Association, 3^(rd)ed. (2000) and thus need not be described in detail herein.

Briefly, formulation of the pharmaceutical compositions of the presentinvention will depend upon the route chosen for administration. Thepharmaceutical compositions utilized in this invention can beadministered by various routes including both enteral and parenteralroutes, including oral, intravenous, intramuscular, subcutaneous,inhalation, topical, sublingual, rectal, intra-arterial, intramedullary,intrathecal, intraventricular, transmucosal, transdermal, intranasal,intraperitoneal, intrapulmonary, and intrauterine.

Oral dosage forms can be formulated as tablets, pills, dragees,capsules, liquids, gels, syrups, slurries, suspensions, and the like,for ingestion by the patient.

Solid formulations of the compositions for oral administration cancontain suitable carriers or excipients, such as carbohydrate or proteinfillers, such as sugars, including lactose, sucrose, mannitol, orsorbitol; starch from corn, wheat, rice, potato, or other plants;cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose,sodium carboxymethylcellulose, or microcrystalline cellulose; gumsincluding arabic and tragacanth; proteins such as gelatin and collagen;inorganics, such as kaolin, calcium carbonate, dicalcium phosphate,sodium chloride; and other agents such as acacia and alginic acid.

Agents that facilitate disintegration and/or solubilization can beadded, such as the cross-linked polyvinyl pyrrolidone, agar, alginicacid, or a salt thereof, such as sodium alginate, microcrystallinecellulose, cornstarch, sodium starch glycolate, and alginic acid.

Tablet binders that can be used include acacia, methylcellulose, sodiumcarboxymethylcellulose, polyvinylpyrrolidone (Povidone™), hydroxypropylmethylcellulose, sucrose, starch and ethylcellulose.

Lubricants that can be used include magnesium stearates, stearic acid,silicone fluid, talc, waxes, oils, and colloidal silica.

Fillers, agents that facilitate disintegration and/or solubilization,tablet binders and lubricants, including the aforementioned, can be usedsingly or in combination.

Solid oral dosage forms need not be uniform throughout. For example,dragee cores can be used in conjunction with suitable coatings, such asconcentrated sugar solutions, which can also contain gum arabic, talc,polyvinylpyrrolidone, carbopol gel, polyethylene glycol, and/or titaniumdioxide, lacquer solutions, and suitable organic solvents or solventmixtures.

Oral dosage forms of the present invention include push-fit capsulesmade of gelatin, as well as soft, sealed capsules made of gelatin and acoating, such as glycerol or sorbitol. Push-fit capsules can containactive ingredients mixed with a filler or binders, such as lactose orstarches, lubricants, such as talc or magnesium stearate, and,optionally, stabilizers. In soft capsules, the active compounds can bedissolved or suspended in suitable liquids, such as fatty oils, liquid,or liquid polyethylene glycol with or without stabilizers.

Additionally, dyestuffs or pigments can be added to the tablets ordragee coatings for product identification or to characterize thequantity of active compound, i.e., dosage.

Liquid formulations of the pharmaceutical compositions for oral(enteral) administration are prepared in water or other aqueous vehiclesand can contain various suspending agents such as methylcellulose,alginates, tragacanth, pectin, kelgin, carrageenan, acacia,polyvinylpyrrolidone, and polyvinyl alcohol. The liquid formulations canalso include solutions, emulsions, syrups and elixirs containing,together with the active compound(s), wetting agents, sweeteners, andcoloring and flavoring agents.

The pharmaceutical compositions of the present invention can also beformulated for parenteral administration. Formulations for parenteraladministration can be in the form of aqueous or non-aqueous isotonicsterile injection solutions or suspensions.

For intravenous injection, water soluble versions of the compounds ofthe present invention are formulated in, or if provided as a lyophilate,mixed with, a physiologically acceptable fluid vehicle, such as 5%dextrose (“D5”), physiologically buffered saline, 0.9% saline, Hanks'solution, or Ringer's solution. Intravenous formulations may includecarriers, excipients or stabilizers including, without limitation,calcium, human serum albumin, citrate, acetate, calcium chloride,carbonate, and other salts.

Intramuscular preparations, e.g. a sterile formulation of a suitablesoluble salt form of the compounds of the present invention, can bedissolved and administered in a pharmaceutical excipient such asWater-for-Injection, 0.9% saline, or 5% glucose solution. Alternatively,a suitable insoluble form of the compound can be prepared andadministered as a suspension in an aqueous base or a pharmaceuticallyacceptable oil base, such as an ester of a long chain fatty acid (e.g.,ethyl oleate), fatty oils such as sesame oil, triglycerides, orliposomes.

Parenteral formulations of the compositions can contain various carrierssuch as vegetable oils, dimethylacetamide, dimethylformamide, ethyllactate, ethyl carbonate, isopropyl myristate, ethanol, polyols(glycerol, propylene glycol, liquid polyethylene glycol, and the like).

Aqueous injection suspensions can also contain substances that increasethe viscosity of the suspension, such as sodium carboxymethyl cellulose,sorbitol, or dextran. Non-lipid polycationic amino polymers can also beused for delivery. Optionally, the suspension can also contain suitablestabilizers or agents that increase the solubility of the compounds toallow for the preparation of highly concentrated solutions.

Pharmaceutical compositions of the present invention can also beformulated to permit injectable, long-term, deposition. Injectable depotforms may be made by forming microencapsulated matrices of the compoundin biodegradable polymers such as polylactide-polyglycolide. Dependingupon the ratio of drug to polymer and the nature of the particularpolymer employed, the rate of drug release can be controlled. Examplesof other biodegradable polymers include poly(orthoesters) andpoly(anhydrides). Depot injectable formulations are also prepared byentrapping the drug in microemulsions that are compatible with bodytissues.

The pharmaceutical compositions of the present invention can beadministered topically. For topical use the compounds of the presentinvention can also be prepared in suitable forms to be applied to theskin, or mucus membranes of the nose and throat, and can take the formof lotions, creams, ointments, liquid sprays or inhalants, drops,tinctures, lozenges, or throat paints. Such topical formulations furthercan include chemical compounds such as dimethylsulfoxide (DMSO) tofacilitate surface penetration of the active ingredient. In othertransdermal formulations, typically in patch-delivered formulations, thepharmaceutically active compound is formulated with one or more skinpenetrants, such as 2-N-methyl-pyrrolidone (NMP) or Azone. A topicalsemi-solid ointment formulation typically contains a concentration ofthe active ingredient from about 1 to 20%, e.g., 5 to 10%, in a carriersuch as a pharmaceutical cream base.

For application to the eyes or ears, the compounds of the presentinvention can be presented in liquid or semi-liquid form formulated inhydrophobic or hydrophilic bases as ointments, creams, lotions, paintsor powders.

For rectal administration the compounds of the present invention can beadministered in the form of suppositories admixed with conventionalcarriers such as cocoa butter, wax or other glyceride.

Inhalation formulations can also readily be formulated. For inhalation,various powder and liquid formulations can be prepared. For aerosolpreparations, a sterile formulation of the compound or salt form of thecompound may be used in inhalers, such as metered dose inhalers, andnebulizers. Aerosolized forms may be especially useful for treatingrespiratory disorders.

Alternatively, the compounds of the present invention can be in powderform for reconstitution in the appropriate pharmaceutically acceptablecarrier at the time of delivery.

The pharmaceutically active compound in the pharmaceutical compositionsof the present invention can be provided as the salt of a variety ofacids, including but not limited to hydrochloric, sulfuric, acetic,lactic, tartaric, malic, and succinic acid. Salts tend to be moresoluble in aqueous or other protonic solvents than are the correspondingfree base forms.

After pharmaceutical compositions have been prepared, they are packagedin an appropriate container and labeled for treatment of an indicatedcondition.

The active compound will be present in an amount effective to achievethe intended purpose. The determination of an effective dose is wellwithin the capability of those skilled in the art.

A “therapeutically effective dose” refers to that amount of activeingredient, for example OSP polypeptide, fusion protein, or fragmentsthereof, antibodies specific for OSP, agonists, antagonists orinhibitors of OSP, which ameliorates the signs or symptoms of thedisease or prevent progression thereof; as would be understood in themedical arts, cure, although desired, is not required.

The therapeutically effective dose of the pharmaceutical agents of thepresent invention can be estimated initially by in vitro tests, such ascell culture assays, followed by assay in model animals, usually mice,rats, rabbits, dogs, or pigs. The animal model can also be used todetermine an initial preferred concentration range and route ofadministration.

For example, the ED50 (the dose therapeutically effective in 50% of thepopulation) and LD50 (the dose lethal to 50% of the population) can bedetermined in one or more cell culture of animal model systems. The doseratio of toxic to therapeutic effects is the therapeutic index, whichcan be expressed as LD50/ED50. Pharmaceutical compositions that exhibitlarge therapeutic indices are preferred.

The data obtained from cell culture assays and animal studies are usedin formulating an initial dosage range for human use, and preferablyprovide a range of circulating concentrations that includes the ED50with little or no toxicity. After administration, or between successiveadministrations, the circulating concentration of active agent varieswithin this range depending upon pharmacokinetic factors well known inthe art, such as the dosage form employed, sensitivity of the patient,and the route of administration.

The exact dosage will be determined by the practitioner, in light offactors specific to the subject requiring treatment Factors that can betaken into account by the practitioner include the severity of thedisease state, general health of the subject, age, weight, gender of thesubject, diet, time and frequency of administration, drugcombination(s), reaction sensitivities, and tolerance/response totherapy. Long-acting pharmaceutical compositions can be administeredevery 3 to 4 days, every week, or once every two weeks depending onhalf-life and clearance rate of the particular formulation.

Normal dosage amounts may vary from 0.1 to 100,000 micrograms, up to atotal dose of about 1 g, depending upon the route of administration.Where the therapeutic agent is a protein or antibody of the presentinvention, the therapeutic protein or antibody agent typically isadministered at a daily dosage of 0.01 mg to 30 mg/kg of body weight ofthe patient (e.g., 1 mg/kg to 5 mg/kg). The pharmaceutical formulationcan be administered in multiple doses per day, if desired, to achievethe total desired daily dose.

Guidance as to particular dosages and methods of delivery is provided inthe literature and generally available to practitioners in the art.Those skilled in the art will employ different formulations fornucleotides than for proteins or their inhibitors. Similarly, deliveryof polynucleotides or polypeptides will be specific to particular cells,conditions, locations, etc.

Conventional methods, known to those of ordinary skill in the art ofmedicine, can be used to administer the pharmaceutical formulation(s) ofthe present invention to the patient. The pharmaceutical compositions ofthe present invention can be administered alone, or in combination withother therapeutic agents or interventions.

Therapeutic Methods

The present invention further provides methods of treating subjectshaving defects in a gene of the invention, e.g., in expression,activity, distribution, localization, and/or solubility, which canmanifest as a disorder of ovarian function. As used herein, “treating”includes all medically-acceptable types of therapeutic intervention,including palliation and prophylaxis (prevention) of disease. The term“treating” encompasses any improvement of a disease, including minorimprovements. These methods are discussed below.

Gene Therapy and Vaccines

The isolated nucleic acids of the present invention can also be used todrive in vivo expression of the polypeptides of the present invention.In vivo expression can be driven from a vector, typically a viralvector, often a vector based upon a replication incompetent retrovirus,an adenovirus, or an adeno-associated virus (AAV), for the purpose ofgene therapy. In vivo expression can also be driven from signalsendogenous to the nucleic acid or from a vector, often a plasmid vector,such as pVAX1 (Invitrogen, Carlsbad, Calif., USA), for purpose of“naked” nucleic acid vaccination, as further described in U.S. Pat. Nos.5,589,466; 5,679,647; 5,804,566; 5,830,877; 5,843,913; 5,880,104;5,958,891; 5,985,847; 6,017,897; 6,110,898; 6,204,250, the disclosuresof which are incorporated herein by reference in their entireties. Forcancer therapy, it is preferred that the vector also be tumor-selective.See, e.g., Doronin et al., J. Virol. 75: 3314-24 (2001).

In another embodiment of the therapeutic methods of the presentinvention, a therapeutically effective amount of a pharmaceuticalcomposition comprising a nucleic acid molecule of the present inventionis administered. The nucleic acid molecule can be delivered in a vectorthat drives expression of an OSP, fusion protein, or fragment thereof,or without such vector. Nucleic acid compositions that can driveexpression of an OSP are administered, for example, to complement adeficiency in the native OSP, or as DNA vaccines. Expression vectorsderived from virus, replication deficient retroviruses, adenovirus,adeno-associated (AAV) virus, herpes virus, or vaccinia virus can beused as can plasmids. See, e.g., Cid-Arregui, supra. In a preferredembodiment, the nucleic acid molecule encodes an OSP having the aminoacid sequence of SEQ ID NO: 129-295, or a fragment, fusion protein,allelic variant or homolog thereof.

In still other therapeutic methods of the present invention,pharmaceutical compositions comprising host cells that express an OSP,fusions, or fragments thereof can be administered. In such cases, thecells are typically autologous, so as to circumvent xenogeneic orallotypic rejection, and are administered to complement defects in OSPproduction or activity. In a preferred embodiment, the nucleic acidmolecules in the cells encode an OSP having the amino acid sequence ofSEQ ID NO: 129-295, or a fragment, fusion protein, allelic variant orhomolog thereof.

Antisense Administration

Antisense nucleic acid compositions, or vectors that drive expression ofan OSG antisense nucleic acid, are administered to downregulatetranscription and/or translation of an OSG in circumstances in whichexcessive production, or production of aberrant protein, is thepathophysiologic basis of disease.

Antisense compositions useful in therapy can have a sequence that iscomplementary to coding or to noncoding regions of an OSG. For example,oligonucleotides derived from the transcription initiation site, e.g.,between positions −10 and +10 from the start site, are preferred.

Catalytic antisense compositions, such as ribozymes, that are capable ofsequence-specific hybridization to OSG transcripts, are also useful intherapy. See, e.g., Phylactou, Adv. Drug Deliv. Rev. 44(2-3): 97-108(2000); Phylactou et al., Hum. Mol. Genet. 7(10): 1649-53 (1998); Rossi,Ciba Found. Symp. 209: 195-204 (1997); and Sigurdsson et al., TrendsBiotechnol. 13(8): 286-9 (1995).

Other nucleic acids useful in the therapeutic methods of the presentinvention are those that are capable of triplex helix formation in ornear the OSG genomic locus. Such triplexing oligonucleotides are able toinhibit transcription. See, e.g., Intody et al., Nucleic Acids Res.28(21): 4283-90 (2000); and McGuffie et al., Cancer Res. 60(14): 3790-9(2000). Pharmaceutical compositions comprising such triplex formingoligos (TFOs) are administered in circumstances in which excessiveproduction, or production of aberrant protein, is a pathophysiologicbasis of disease.

In a preferred embodiment, the antisense molecule is derived from anucleic acid molecule encoding an OSP, preferably an OSP comprising anamino acid sequence of SEQ ID NO: 129-295, or a fragment, allelicvariant or homolog thereof. In a more preferred embodiment, theantisense molecule is derived from a nucleic acid molecule having anucleotide sequence of SEQ ID NO: 1-128, or a part, allelic variant,substantially similar or hybridizing nucleic acid thereof.

Polypeptide Administration

In one embodiment of the therapeutic methods of the present invention, atherapeutically effective amount of a pharmaceutical compositioncomprising an OSP, a fusion protein, fragment, analog or derivativethereof is administered to a subject with a clinically-significant OSPdefect.

Protein compositions are administered, for example, to complement adeficiency in native OSP. In other embodiments, protein compositions areadministered as a vaccine to elicit a humoral and/or cellular immuneresponse to OSP. The immune response can be used to modulate activity ofOSP or, depending on the immunogen, to immunize against aberrant oraberrantly expressed forms, such as mutant or inappropriately expressedisoforms. In yet other embodiments, protein fusions having a toxicmoiety are administered to ablate cells that aberrantly accumulate OSP.

In a preferred embodiment, the polypeptide administered is an OSPcomprising an amino acid sequence of SEQ ID NO: 129-295, or a fusionprotein, allelic variant, homolog, analog or derivative thereof. In amore preferred embodiment, the polypeptide is encoded by a nucleic acidmolecule having a nucleotide sequence of SEQ ID NO: 1-128, or a part,allelic variant, substantially similar or hybridizing nucleic acidthereof.

Antibody, Agonist and Antagonist Administration

In another embodiment of the therapeutic methods of the presentinvention, a therapeutically effective amount of a pharmaceuticalcomposition comprising an antibody (including fragment or derivativethereof) of the present invention is administered. As is well known,antibody compositions are administered, for example, to antagonizeactivity of OSP, or to target therapeutic agents to sites of OSPpresence and/or accumulation. In a preferred embodiment, the antibodyspecifically binds to an OSP comprising an amino acid sequence of SEQ IDNO: 129-295, or a fusion protein, allelic variant, homolog, analog orderivative thereof. In a more preferred embodiment, the antibodyspecifically binds to an OSP encoded by a nucleic acid molecule having anucleotide sequence of SEQ ID NO: 1-128, or a part, allelic variant,substantially similar or hybridizing nucleic acid thereof.

The present invention also provides methods for identifying modulatorswhich bind to an OSP or have a modulatory effect on the expression oractivity of an OSP. Modulators which decrease the expression or activityof OSP (antagonists) are believed to be useful in treating ovariancancer. Such screening assays are known to those of skill in the art andinclude, without limitation, cell-based assays and cell-free assays.Small molecules predicted via computer imaging to specifically bind toregions of an OSP can also be designed, synthesized and tested for usein the imaging and treatment of ovarian cancer. Further, libraries ofmolecules can be screened for potential anticancer agents by assessingthe ability of the molecule to bind to the OSPs identified herein.Molecules identified in the library as being capable of binding to anOSP are key candidates for further evaluation for use in the treatmentof ovarian cancer. In a preferred embodiment, these molecules willdownregulate expression and/or activity of an OSP in cells.

In another embodiment of the therapeutic methods of the presentinvention, a pharmaceutical composition comprising a non-antibodyantagonist of OSP is administered. Antagonists of OSP can be producedusing methods generally known in the art. In particular, purified OSPcan be used to screen libraries of pharmaceutical agents, oftencombinatorial libraries of small molecules, to identify those thatspecifically bind and antagonize at least one activity of an OSP.

In other embodiments a pharmaceutical composition comprising an agonistof an OSP is administered. Agonists can be identified using methodsanalogous to those used to identify antagonists.

In a preferred embodiment, the antagonist or agonist specifically bindsto and antagonizes or agonizes, respectively, an OSP comprising an aminoacid sequence of SEQ ID NO: 129-295, or a fusion protein, allelicvariant, homolog, analog or derivative thereof. In a more preferredembodiment, the antagonist or agonist specifically binds to andantagonizes or agonizes, respectively, an OSP encoded by a nucleic acidmolecule having a nucleotide sequence of SEQ ID NO: 1-128, or a part,allelic variant, substantially similar or hybridizing nucleic acidthereof.

Targeting Ovarian Tissue

The invention also provides a method in which a polypeptide of theinvention, or an antibody thereto, is linked to a therapeutic agent suchthat it can be delivered to the ovarian or to specific cells in theovarian. In a preferred embodiment, an anti-OSP antibody is linked to atherapeutic agent and is administered to a patient in need of suchtherapeutic agent. The therapeutic agent may be a toxin, if ovariantissue needs to be selectively destroyed. This would be useful fortargeting and killing ovarian cancer cells. In another embodiment, thetherapeutic agent may be a growth or differentiation factor, which wouldbe useful for promoting ovarian cell function.

In another embodiment, an anti-OSP antibody may be linked to an imagingagent that can be detected using, e.g., magnetic resonance imaging, CTor PET. This would be useful for determining and monitoring ovarianfunction, identifying ovarian cancer tumors, and identifyingnoncancerous ovarian diseases.

EXAMPLES Example 1a Alternative Splice Variants

We identified gene transcripts using the Gencarta™ tools (Compugen Ltd.,Tel Aviv, Israel) and a variety of public and proprietary databases.These splice variants are either sequences which differ from apreviously defined sequence or new uses of known sequences. In generalrelated variants are annotated as DEX0455_XXX.nt.1, DEX0455_XXX.nt.2,DEX0455_XXX.nt.3, etc. The variant DNA sequences encode proteins whichdiffer from a previously defined protein sequence. In relation to thenucleotide sequence naming convention, protein variants are annotated asDEX0455_XXX.aa.1, DEX0455_XXX.aa.2, etc., wherein transcriptDEX0455_XXX.nt1 encodes protein DEX0455_XXX.aa.1. A single transcriptmay encode a protein from an alternate Open Reading Fram (ORF) which isdesignated DEX0455_XXX.orf.1. Additionally, multiple transcripts mayencode for a single protein. In this case, DEX0455_XXX.nt.1 andDEX0455_XXX.nt.2 will both be associated with DEX0455_XXX.aa.1.

The mapping of the nucleic acid (“NT”) SEQ ID NO; DEX ID; chromosomallocation (if known); open reading frame (ORF) location; amino acid(“AA”) SEQ ID NO; AA DEX ID; are shown in the table below. SEQ SEQ ID IDNO DEX ID Chromo Map ORF Loc NO DEX ID 1 DEX0455_001.nt.1 X;47722965-47733965 1624-2937 129 DEX0455_001.orf.1 1 DEX0455_001.nt.1 X;47722965-47733965  322-1035 130 DEX0455_001.aa.1 2 DEX0455_002.nt.117q11.1 217-915 131 DEX0455_002.aa.1 3 DEX0455_003.nt.1 10p11.23 132-476132 DEX0455_003.aa.1 4 DEX0455_004.nt.1 3q29 7357-7809 133DEX0455_004.orf.1 4 DEX0455_004.nt.1 3q29 2974-5074 134 DEX0455_004.aa.15 DEX0455_004.nt.2 3q29 6201-6653 135 DEX0455_004.orf.2 5DEX0455_004.nt.2 3q29 2968-5257 136 DEX0455_004.aa.2 6 DEX0455_005.nt.12q13  854-1267 137 DEX0455_005.aa.1 7 DEX0455_005.nt.2 2q13  853-1270137 DEX0455_005.aa.1 8 DEX0455_006.nt.1 9q22.1  730-1266 138DEX0455_006.aa.1 9 DEX0455_007.nt.1 19q13.41  1-882 139DEX0455_007.orf.1 9 DEX0455_007.nt.1 19q13.41  1-885 140DEX0455_007.aa.1 10 DEX0455_008.nt.1 4q27  869-1138 141 DEX0455_008.aa.111 DEX0455_009.nt.1 20p12.2   1-1123 142 DEX0455_009.aa.1 12DEX0455_010.nt.1 Un_6; 1484154-1498876 341-784 143 DEX0455_010.orf.1 12DEX0455_010.nt.1 Un_6; 1484154-1498876 151-370 144 DEX0455_010.aa.1 13DEX0455_010.nt.2 Un_6; 1484154-1498876 49-621 145 DEX0455_010.orf.2 13DEX0455_010.nt.2 Un_6; 1484154-1498876 151-490 146 DEX0455_010.aa.2 14DEX0455_011.nt.1 19q13.31  1-384 147 DEX0455_011.aa.1 15DEX0455_012.nt.1 1q32.1 207-974 148 DEX0455_012.aa.1 16 DEX0455_012.nt.21q32.1 102-851 149 DEX0455_012.orf.2 16 DEX0455_012.nt.2 1q32.1 206-1415 150 DEX0455_012.aa.2 17 DEX0455_013.nt.1 12p12.3  10-666 151DEX0455_013.aa.1 18 DEX0455_013.nt.2 12p12.3 124-639 152DEX0455_013.aa.2 19 DEX0455_014.nt.1 1q42.2  880-1866 153DEX0455_014.orf.1 19 DEX0455_014.nt.1 1q42.2  82-1870 154DEX0455_014.aa.1 20 DEX0455_015.nt.1 12q13.2  1-255 155 DEX0455_015.aa.121 DEX0455_016.nt.1 1p31.1 104-868 156 DEX0455_016.aa.1 22DEX0455_017.nt.1 1p33 102-623 157 DEX0455_017.aa.1 23 DEX0455_018.nt.19q34.11  209-1270 158 DEX0455_018.aa.1 24 DEX0455_018.nt.2 9q34.11 682-2148 159 DEX0455_018.aa.2 25 DEX0455_019.nt.1 11q13.4  66-926 160DEX0455_019.aa.1 26 DEX0455_020.nt.1 19p13.11 365-793 161DEX0455_020.aa.1 27 DEX0455_020.nt.2 19p13.11  688-1035 162DEX0455_020.orf.2 27 DEX0455_020.nt.2 19p13.11 474-678 163DEX0455_020.aa.2 28 DEX0455_021.nt.1 1p36.11 175-486 164DEX0455_021.orf.1 28 DEX0455_021.nt.1 1p36.11  1-250 165DEX0455_021.aa.1 29 DEX0455_021.nt.2 1p36.11  190-1269 166DEX0455_021.aa.2 30 DEX0455_021.nt.3 1p36.11  46-1173 167DEX0455_021.orf.3 30 DEX0455_021.nt.3 1p36.11  189-1590 168DEX0455_021.aa.3 31 DEX0455_021.nt.4 1p36.11  190-1173 169DEX0455_021.aa.4 32 DEX0455_022.nt.1 19p13.12 109-642 170DEX0455_022.aa.1 33 DEX0455_022.nt.2 19p13.12  70-492 171DEX0455_022.orf.2 33 DEX0455_022.nt.2 19p13.12 108-675 172DEX0455_022.aa.2 34 DEX0455_022.nt.3 19p13.12  91-324 173DEX0455_022.aa.3 35 DEX0455_023.nt.1 7q11.21 609-956 174DEX0455_023.aa.1 36 DEX0455_024.nt.1 2p13.3  486-1569 175DEX0455_024.aa.1 37 DEX0455_024.nt.2 2p13.3 469-999 176 DEX0455_024.aa.238 DEX0455_025.nt.1 17q24.3  475-1614 177 DEX0455_025.aa.1 39DEX0455_025.nt.2 17q24.3  328-1509 178 DEX0455_025.orf.2 39DEX0455_025.nt.2 17q24.3  474-2514 179 DEX0455_025.aa.2 40DEX0455_025.nt.3 17q24.3  474-1617 177 DEX0455_025.aa.1 41DEX0455_025.nt.4 17q24.3  474-1617 177 DEX0455_025.aa.1 42DEX0455_026.nt.1 2q32.2  3-218 180 DEX0455_026.orf.1 42 DEX0455_026.nt.12q32.2  1-236 181 DEX0455_026.aa.1 43 DEX0455_027.nt.1 2q24.3  986-1507182 DEX0455_027.orf.1 43 DEX0455_027.nt.1 2q24.3  16-128 183DEX0455_027.aa.1 44 DEX0455_028.nt.1 9p24.3 141-785 184 DEX0455_028.aa.145 DEX0455_029.nt.1 9q21.11 4134-4532 185 DEX0455_029.orf.1 45DEX0455_029.nt.1 9q21.11 2985-5847 186 DEX0455_029.aa.1 46DEX0455_029.nt.2 9q21.11 4562-5143 187 DEX0455_029.orf.2 46DEX0455_029.nt.2 9q21.11 2962-5149 188 DEX0455_029.aa.2 47DEX0455_030.nt.1 16p11.2  188-1123 189 DEX0455_030.aa.1 48DEX0455_030.nt.2 16p11.2  82-627 190 DEX0455_030.aa.2 49DEX0455_031.nt.1 12p13.31  135-1013 191 DEX0455_031.orf.1 49DEX0455_031.nt.1 12p13.31  248-2156 192 DEX0455_031.aa.1 50DEX0455_031.nt.2 12p13.31 248-749 193 DEX0455_031.aa.2 50DEX0455_031.nt.2 12p13.31 1325-2239 194 DEX0455_031.orf.2 51DEX0455_031.nt.3 12p13.31  1-582 195 DEX0455_031.aa.3 52DEX0455_032.nt.1 7q31.1  39-761 196 DEX0455_032.aa.1 53 DEX0455_033.nt.11p34.1 161-943 197 DEX0455_033.aa.1 54 DEX0455_034.nt.1 15q21.1 197-1693 198 DEX0455_034.aa.1 55 DEX0455_034.nt.2 15q21.1   1-1497 198DEX0455_034.aa.1 56 DEX0455_034.nt.3 15q21.1  197-1228 199DEX0455_034.aa.3 57 DEX0455_034.nt.4 15q21.1   2-1438 200DEX0455_034.aa.4 58 DEX0455_035.nt.1 10q22.1 102-464 201DEX0455_035.aa.1 59 DEX0455_035.nt.2 10q22.1  755-1201 202DEX0455_035.orf.2 59 DEX0455_035.nt.2 10q22.1 330-696 203DEX0455_035.aa.2 60 DEX0455_035.nt.3 10q22.1  634-1080 204DEX0455_035.orf.3 60 DEX0455_035.nt.3 10q22.1 269-575 205DEX0455_035.aa.3 61 DEX0455_036.nt.1 19p13.2  86-370 206DEX0455_036.orf.1 61 DEX0455_036.nt.1 19p13.2  58-389 207DEX0455_036.aa.1 62 DEX0455_036.nt.2 19p13.2  295-4749 208DEX0455_036.aa.2 63 DEX0455_036.nt.3 19p13.2  3-335 209DEX0455_036.orf.3 63 DEX0455_036.nt.3 19p13.2  88-352 210DEX0455_036.aa.3 64 DEX0455_036.nt.4 19p13.2  77-352 211DEX0455_036.orf.4 64 DEX0455_036.nt.4 19p13.2  1-253 212DEX0455_036.aa.4 65 DEX0455_037.nt.1 9 113-787 213 DEX0455_037.aa.1 66DEX0455_037.nt.2 9   2-1048 214 DEX0455_037.orf.2 66 DEX0455_037.nt.2 9 112-1354 215 DEX0455_037.aa.2 67 DEX0455_037.nt.3 9  113-1342 216DEX0455_037.aa.3 68 DEX0455_037.nt.4 9  2-410 217 DEX0455_037.aa.4 69DEX0455_037.nt.5 9  3-452 218 DEX0455_037.aa.5 70 DEX0455_037.nt.6 9113-784 219 DEX0455_037.aa.6 71 DEX0455_037.nt.7 9  113-1555 220DEX0455_037.aa.7 72 DEX0455_038.nt.1 20p12.1  298-3561 221DEX0455_038.aa.1 73 DEX0455_038.nt.2 20p12.1  298-3564 221DEX0455_038.aa.1 74 DEX0455_038.nt.3 20p12.1   1-1320 222DEX0455_038.orf.3 74 DEX0455_038.nt.3 20p12.1  298-1863 223DEX0455_038.aa.3 75 DEX0455_039.nt.1 19q13.2  2-496 224 DEX0455_039.aa.176 DEX0455_039.nt.2 19q13.2  2-787 225 DEX0455_039.aa.2 77DEX0455_040.nt.1 19q13.2 299-991 226 DEX0455_040.orf.1 77DEX0455_040.nt.1 19q13.2 352-991 227 DEX0455_040.aa.1 78DEX0455_040.nt.2 19q13.2  770-1495 228 DEX0455_040.aa.2 79DEX0455_041.nt.1 20q11.23  54-212 229 DEX0455_041.orf.1 79DEX0455_041.nt.1 20q11.23  7-138 230 DEX0455_041.aa.1 80DEX0455_041.nt.2 20q11.23  11-208 231 DEX0455_041.orf.2 80DEX0455_041.nt.2 20q11.23  1-107 232 DEX0455_041.aa.2 81DEX0455_042.nt.1 4q22.1  90-437 233 DEX0455_042.orf.1 81DEX0455_042.nt.1 4q22.1  70-439 234 DEX0455_042.aa.1 82 DEX0455_043.nt.11q42.12 511-768 235 DEX0455_043.orf.1 82 DEX0455_043.nt.1 1q42.12  1-93236 DEX0455_043.aa.1 83 DEX0455_043.nt.2 1q42.12 413-787 237DEX0455_043.orf.2 83 DEX0455_043.nt.2 1q42.12  1-93 236 DEX0455_043.aa.184 DEX0455_043.nt.3 1q42.12 1220-1531 238 DEX0455_043.orf.3 84DEX0455_043.nt.3 1q42.12  1-93 236 DEX0455_043.aa.1 85 DEX0455_044.nt.117q25.3 445-627 239 DEX0455_044.aa.1 86 DEX0455_045.nt.1 16p12.3  1-579240 DEX0455_045.orf.1 86 DEX0455_045.nt.1 16p12.3  1-492 241DEX0455_045.aa.1 87 DEX0455_046.nt.1 17q21.32  709-1389 242DEX0455_046.orf.1 87 DEX0455_046.nt.1 17q21.32  802-1389 243DEX0455_046.aa.1 88 DEX0455_047.nt.1 8p23.1 2887-3195 244DEX0455_047.orf.1 88 DEX0455_047.nt.1 8p23.1 136-334 245DEX0455_047.aa.1 89 DEX0455_047.nt.2 8p23.1 1091-1399 246DEX0455_047.orf.2 89 DEX0455_047.nt.2 8p23.1  19-102 247DEX0455_047.aa.2 90 DEX0455_048.nt.1 X; 150645762-150649651  84-545 248DEX0455_048.aa.1 91 DEX0455_048.nt.2 X; 150645762-150649651 286-813 249DEX0455_048.orf.2 91 DEX0455_048.nt.2 X; 150645762-150649651  1-817 250DEX0455_048.aa.2 92 DEX0455_049.nt.1 2p21 1183-1986 251 DEX0455_049.aa.193 DEX0455_049.nt.2 2p21  378-1403 252 DEX0455_049.aa.2 94DEX0455_049.nt.3 2p21  808-1527 253 DEX0455_049.aa.3 95 DEX0455_049.nt.42p21   1-1170 254 DEX0455_049.aa.4 96 DEX0455_049.nt.5 2p21  179-1120255 DEX0455_049.aa.5 97 DEX0455_050.nt.1 7p22.1 186-551 256DEX0455_050.orf.1 97 DEX0455_050.nt.1 7p22.1  1-149 257 DEX0455_050.aa.198 DEX0455_051.nt.1 19   1-1788 258 DEX0455_051.aa.1 99 DEX0455_051.nt.219   1-1224 259 DEX0455_051.aa.2 100 DEX0455_051.nt.3 19   1-1410 260DEX0455_051.aa.3 101 DEX0455_051.nt.4 19   1-1224 259 DEX0455_051.aa.2101 DEX0455_051.nt.4 19   1-1422 261 DEX0455_051.orf.4 102DEX0455_051.nt.5 19   1-1224 259 DEX0455_051.aa.2 102 DEX0455_051.nt.519   1-1422 262 DEX0455_051.orf.5 103 DEX0455_051.nt.6 19   1-1224 259DEX0455_051.aa.2 103 DEX0455_051.nt.6 19   1-1422 263 DEX0455_051.orf.6104 DEX0455_052.nt.1 19  13-1422 264 DEX0455_052.aa.1 105DEX0455_052.nt.2 19  13-1518 265 DEX0455_052.aa.2 106 DEX0455_052.nt.319  188-1831 266 DEX0455_052.aa.3 107 DEX0455_052.nt.4 19 100-930 267DEX0455_052.aa.4 108 DEX0455_053.nt.1 1p12  1-846 268 DEX0455_053.aa.1109 DEX0455_053.nt.2 1p12  1-177 269 DEX0455_053.aa.2 109DEX0455_053.nt.2 1p12  253-1008 270 DEX0455_053.aa.3 110DEX0455_054.nt.1 15q24.3 1218-1682 271 DEX0455_054.orf.1 110DEX0455_054.nt.1 15q24.3 1038-1362 272 DEX0455_054.aa.1 111DEX0455_054.nt.2 15q24.3 410-874 273 DEX0455_054.orf.2 111DEX0455_054.nt.2 15q24.3 122-554 274 DEX0455_054.aa.2 112DEX0455_055.nt.1 1  812-1570 275 DEX0455_055.aa.1 113 DEX0455_055.nt.2 1 388-1470 276 DEX0455_055.aa.2 114 DEX0455_055.nt.3 1p34.2 402-902 277DEX0455_055.aa.3 115 DEX0455_056.nt.1 7q31.1  626-2533 278DEX0455_056.orf.1 115 DEX0455_056.nt.1 7q31.1  670-3283 279DEX0455_056.aa.1 116 DEX0455_056.nt.2 7q31.1  671-3043 280DEX0455_056.aa.2 117 DEX0455_057.nt.1 1q21.3 146-511 281DEX0455_057.orf.1 117 DEX0455_057.nt.1 1q21.3  1-513 282DEX0455_057.aa.1 118 DEX0455_057.nt.2 1q21.3 405-681 283DEX0455_057.aa.2 119 DEX0455_058.nt.1 1q42.12 1208-1405 284DEX0455_058.orf.1 119 DEX0455_058.nt.1 1q42.12 315-513 285DEX0455_058.aa.1 120 DEX0455_059.nt.1 19p13.11  294-1382 286DEX0455_059.orf.1 120 DEX0455_059.nt.1 19p13.11  1-352 287DEX0455_059.aa.1 121 DEX0455_059.nt.2 19p13.11  596-1093 288DEX0455_059.orf.2 121 DEX0455_059.nt.2 19p13.11  1-352 287DEX0455_059.aa.1 122 DEX0455_060.nt.1 21q21.1  3-623 289DEX0455_060.aa.1 123 DEX0455_061.nt.1 10q11.21 1564-2619 290DEX0455_061.aa.1 124 DEX0455_061.nt.2 10q11.21 2449-3231 291DEX0455_061.aa.2 125 DEX0455_061.nt.3 10q11.21 2449-3255 292DEX0455_061.aa.3 126 DEX0455_061.nt.4 10q11.21 1045-1443 293DEX0455_061.aa.4 127 DEX0455_061.nt.5 10q11.21  842-1330 294DEX0455_061.orf.5 127 DEX0455_061.nt.5 10q11.21 1740-2142 293DEX0455_061.aa.4 128 DEX0455_062.nt.1 2p25.1  120-1592 295DEX0455_062.aa.1

The polypeptides of the present invention were analyzed and thefollowing attributes were identified; specifically, epitopes, posttranslational modifications, signal peptides and transmembrane domains.Antigenicity (Epitope) prediction was performed through the antigenicmodule in the EMBOSS package. Rice, P., EMBOSS: The European MolecularBiology Open Software Suite, Trends in Genetics 16(6): 276-277 (2000).The antigenic module predicts potentially antigenic regions of a proteinsequence, using the method of Kolaskar and Tongaonkar. Kolaskar, A S andTongaonkar, P C., A semi-empirical method for prediction of antigenicdeterminants on protein antigens, FEBS Letters 276: 172-174 (1990).Examples of post-translational modifications (PTMs) and other motifs ofthe OSPs of this invention are listed below. In addition, antibodiesthat specifically bind such post-translational modifications may beuseful as a diagnostic or as therapeutic. The PTMs and other motifs werepredicted by using the ProSite Dictionary of Proteins Sites and Patterns(Bairoch et al., Nucleic Acids Res. 25(1):217-221 (1997)), the followingmotifs, including PTMs, were predicted for the OSPs of the invention Thesignal peptides were detected by using the SignalP 2.0, see Nielsen etal., Protein Engineering 12, 3-9 (1999). Prediction of transmembranehelices in proteins was performed by the application TMHMM 2.0,“currently the best performing transmembrane prediction program”,according to authors (Krogh et al, Journal of Molecular Biology,305(3):567-580, (2001); Moller et al., Bioinformatics, 17(7):646-653,(2001); Sonnhammer, et al., A hidden Markov model for predictingtransmembrane helices in protein sequences in Glasgow, et al. Ed.Proceedings of the Sixth International Conference on Intelligent Systemsfor Molecular Biology, pages 175-182, Menlo Park, Calif., 1998. AAAIPress. The PSORT II program may also be used to predict cellularlocalizations. Horton et al., Intelligent Systems for Molecular Biology5: 147-152 (1997). The table below includes the following sequenceannotations: Signal peptide presence; TM (number of membrane domain,topology in orientation and position); Amino acid location and antigenicindex (location, AI score); PTM and other motifs (type, amino acidresidue locations); and functional domains (type, amino acid residuelocations). DEX ID Sig P TMHMM Antigenicity PTM DomainsDEX0455_001.orf.1 N 0 - 333-345, CK2_PHOSPHO_SITE 104-107; PRICHEXTENSNo1-438; 1.127; PKC_PHOSPHO_SITE 284-286; 111-128; 155-162,CAMP_PHOSPHO_SITE 85-88; PRO_RICH_2 185-351; 1.105; CK2_PHOSPHO_SITE352-355; PRICHEXTENSN 1-13; 184-208, CK2_PHOSPHO_SITE 43-46;PRICHEXTENSN 1.14; PKC_PHOSPHO_SITE 430-432; 63-75; 231-239, MYRISTYL138-143; MYRISTYL PRICHEXTENSN 1.049; 265-270; ASN_GLYCOSYLATION206-231; 56-63, 167-170; PKC_PHOSPHO_SITE PRO_RICH_1 1-75; 1.067;216-218; MYRISTYL 260-265; 170-176, TYR_PHOSPHO_SITE 200-206; 1.117;MYRISTYL 179-184; 38-47, PKC_PHOSPHO_SITE 84-86; 1.115; PKC_PHOSPHO_SITE153-155; 75-81, PKC_PHOSPHO_SITE 163-165; 1.069; CK2_PHOSPHO_SITE284-287; 108-119, MYRISTYL 267-272; 1.16; 305-311, 1.041; 273-283,1.106; 241-256, 1.161; 4-36, 1.186; 323-329, 1.094; 290-302, 1.123;383-435, 1.147; 122-131, 1.09; 211-217, 1.039; DEX0455_001.aa.1 N 0 -164-217, MYRISTYL 194-199; MYRISTYL o1-237; 1.189; 5-10;PKC_PHOSPHO_SITE 88-90; 14-30, PKC_PHOSPHO_SITE 47-49; 1.076;CK2_PHOSPHO_SITE 41-44; 79-85, LEUCINE_ZIPPER 157-178; 1.054; MYRISTYL198-203; 64-74, PKC_PHOSPHO_SITE 29-31; 1.136; MYRISTYL 187-192;148-161, PKC_PHOSPHO_SITE 235-237; 1.094; CK2_PHOSPHO_SITE 205-208;89-114, 1.145; 116-138, 1.139; 43-61, 1.159; 33-39, 1.034; 4-11, 1.088;DEX0455_002.aa.1 N 0 - 174-212, CK2_PHOSPHO_SITE 159-162;TONB_DEPENDENT_REC_1 o1-233; 1.218; MYRISTYL 139-144; MYRISTYL 1-49;88-148, 112-117; MYRISTYL 83-88; GALAPTIN 165-186; 1.133;ASN_GLYCOSYLATION 47-50; GLECT 103-233; 153-158, MYRISTYL 181-186;MYRISTYL Gal- 1.07; 61-66; bind_lectin 67-81, 104-233; 1.137; 46-65,1.141; 9-44, 1.202; DEX0455_003.aa.1 N 0 - 9-18, CAMP_PHOSPHO_SITE21-24; ARG_RICH 18-104; o1-115; 1.083; CK2_PHOSPHO_SITE 24-27; 30-51,MYRISTYL 57-62; 1.14; PKC_PHOSPHO_SITE 32-34; 56-82, CK2_PHOSPHO_SITE43-46; 1.155; MYRISTYL 25-30; 104-111, PKC_PHOSPHO_SITE 4-6; 1.084;AMIDATION 101-104; PKC_PHOSPHO_SITE 93-95; PKC_PHOSPHO_SITE 109-111;AMIDATION 4-7; DEX0455_004.orf.1 N 1 - 112-143, MYRISTYL 96-101; o1-54;1.199; PKC_PHOSPHO_SITE 145-147; tm55-74; 5-12, MYRISTYL 82-87; MYRISTYLi75-151; 1.074; 105-110; PKC_PHOSPHO_SITE 40-104, 25-27;CK2_PHOSPHO_SITE 1.27; 143-146; 14-37, 1.097; DEX0455_004.aa.1 N 2 -245-261, CK2_PHOSPHO_SITE 440-443; RIBOSOMAL_S2_1 o1-594; 1.17;CK2_PHOSPHO_SITE 36-39; 245-256; tm595-617; 51-68, PKC_PHOSPHO_SITE641-643; LYS_RICH 9-22; i618-666; 1.161; MYRISTYL 264-269; tm667-689;429-437, PKC_PHOSPHO_SITE 28-30; o690-699; 1.15; ASN_GLYCOSYLATION471-474; 202-222, ASN_GLYCOSYLATION 628-631; 1.139; MYRISTYL 591-596;533-553, PKC_PHOSPHO_SITE 210-212; 1.095; CAMP_PHOSPHO_SITE 15-18;102-115, ASN_GLYCOSYLATION 569-572; 1.182; CK2_PHOSPHO_SITE 140-143;186-193, PKC_PHOSPHO_SITE 302-304; 1.076; MYRISTYL 557-562; 121-140,AMIDATION 19-22; 1.245; ASN_GLYCOSYLATION 297-300; 333-341, AMIDATION197-200; 1.129; CAMP_PHOSPHO_SITE 587-590; 375-383, CK2_PHOSPHO_SITE542-545; 1.117; PKC_PHOSPHO_SITE 420-422; 265-319, PKC_PHOSPHO_SITE70-72; 1.148; MYRISTYL 530-535; 142-174, PKC_PHOSPHO_SITE 560-562;1.138; MYRISTYL 256-261; 70-98, CAMP_PHOSPHO_SITE 16-19; 1.151; MYRISTYL625-630; 345-354, PKC_PHOSPHO_SITE 527-529; 1.089; MYRISTYL 93-98;579-588, PKC_PHOSPHO_SOTE 19-21; 1.236; PKC_PHOSPHO_SITE 514-516;445-458, TYR_PHOSPHO_SITE 149-155; 1.242; 515-531, 1.129; 398-405,1.098; 690-696, 1.182; 593-617, 1.232; 224-243, 1.183; 629-688, 1.194;408-413, 1.058; 475-512, 1.147; 462-473, 1.227; 23-34, 1.175; 363-369,1.038; DEX0455_004.orf.2 N 1 - 14-37, CK2_PHOSPHO_SITE 143-146; o1-54;1.097; MYRISTYL 96-101; tm55-74; 40-104, PKC_PHOSPHO_SITE 25-27;i75-151; 1.27; MYRISTYL 105-110; MYRISTYL 112-143, 82-87;PKC_PHOSPHO_SITE 1.199; 145-147; 5-12, 1.074; DEX0455_004.aa.2 N 9 -713-724, PKC_PHOSPHO_SITE 257-259; N4_MTASE 609-614; o1-210; 1.168;MYRISTYL 14-19; MYRISTYL tm211-233; 19-28, 173-178; CK2_PHOSPHO_SITEi234-282; 1.088; 676-679; PKC_PHOSPHO_SITE tm283-305; 131-153, 620-622;PKC_PHOSPHO_SITE o306-324; 1.129; 143-145; ASN_GLYCOSYLATION tm325-347;746-755, 418-421; PKC_PHOSPHO_SITE i348-367; 1.027; 176-178; MYRISTYL207-212; tm368-385; 209-233, ASN_GLYCOSYLATION 87-90; o386-543; 1.232;CAMP_PHOSPHO_SITE 203-206; tm544-566; 604-653, MYRISTYL 161-166;MYRISTYL i567-578; 1.189; 13-18; ASN_GLYCOSYLATION tm579-599; 78-89,493-496; MYRISTYL 691-696; o600-613; 1.227; TYR_PHOSPHO_SITE 755-761;tm614-633; 484-491, PKC_PHOSPHO_SITE 676-678; i634-679; 1.123; MYRISTYL241-246; tm680-699; 402-459, ASN_GLYCOSYLATION 363-366; o700-703; 1.205;CK2_PHOSPHO_SITE 466-469; tm704-721; 497-519, PKC_PHOSPHO_SITE 594-596;i722-762; 1.232; ASN_GLYCOSYLATION 312-315; 367-394, ASN_GLYCOSYLATION244-247; 1.253; CK2_PHOSPHO_SITE 56-59; 195-204, CK2_PHOSPHO_SITE320-323; 1.236; CK2_PHOSPHO_SITE 506-509; 91-128, PKC_PHOSPHO_SITE425-427; 1.147; PKC_PHOSPHO_SITE 721-723; 657-705, MYRISTYL 712-717;1.254; PKC_PHOSPHO_SITE 130-132; 245-313, ASN_GLYCOSYLATION 185-188;1.194; PKC_PHOSPHO_SITE 506-508; 577-601, 1.285; 555-569, 1.252;523-553, 1.135; 737-744, 1.1; 61-74, 1.242; 156-169, 1.143; 45-53, 1.15;323-353, 1.237; 472-480, 1.153; DEX0455_005.aa.1 N 0 - 19-29,PKC_PHOSPHO_SITE 87-89; o1-138; 1.121; MYRISTYL 21-26; 125-132,PKC_PHOSPHO_SITE 131-133; 1.063; MYRISTYL 102-107; 4-9, 1.045;CK2_PHOSPHO_SITE 38-41; 45-61, CK2_PHOSPHO_SITE 29-32; 1.116; 88-107,1.22; 76-85, 1.064; DEX0455_006.aa.1 N 0 - 34-45, CAMP_PHOSPHO_SITE62-65; o1-179; 1.149; CK2_PHOSPHO_SITE 110-113; 92-99, AMIDATION138-141; 1.162; CK2_PHOSPHO_SITE 67-70; 8-14, TYR_PHOSPHO_SITE 88-95;1.034; CK2_PHOSPHO_SITE 74-77; 117-135, PKC_PHOSPHO_SITE 112-114; 1.172;MYRISTYL 36-41; 49-61, CAMP_PHOSPHO_SITE 127-130; 1.175;CK2_PHOSPHO_SITE 106-109; 168-176, MYRISTYL 133-138; 1.097; 104-110,1.069; 77-85, 1.119; 143-155, 1.15; DEX0455_007.orf.1 N 0 - 4-23,PKC_PHOSPHO_SITE 24-26; o1-294; 1.139; CK2_PHOSPHO_SITE 71-74; 194-201,MYRISTYL 231-236; 1.095; CK2_PHOSPHO_SITE 203-206; 133-176,PKC_PHOSPHO_SITE 270-272; 1.151; PKC_PHOSPHO_SITE 131-133; 39-45,CK2_PHOSPHO_SITE 189-192; 1.069; MYRISTYL 278-283; 58-68,CK2_PHOSPHO_SITE 24-27; 1.056; MYRISTYL 201-206; MYRISTYL 244-261,266-271; MYRISTYL 120-125; 1.123; CK2_PHOSPHO_SITE 56-59; 78-120,CAMP_PHOSPHO_SITE 132-135; 1.147; DEX0455_007.aa.1 N 0 - 4-23, MYRISTYL266-271; o1-294; 1.139; CAMP_PHOSPHO_SITE 132-135; 133-176,PKC_PHOSPHO_SITE 131-133; 1.151; MYRISTYL 278-283; 194-201,CK2_PHOSPHO_SITE 24-27; 1.095; MYRISTYL 120-125; 39-45, CK2_PHOSPHO_SITE189-192; 1.069; MYRISTYL 201-206; 244-261, CK2_PHOSPHO_SITE 71-74;1.123; PKC_PHOSPHO_SITE 270-272; 58-68, CK2_PHOSPHO_SITE 203-206; 1.056;MYRISTYL 231-236; 78-120, PKC_PHOSPHO_SITE 24-26; 1.147;CK2_PHOSPHO_SITE 56-59; DEX0455_008.aa.1 N 0 - 43-78, CK2_PHOSPHO_SITE57-60; HORMA 14-72; o1-90; 1.171; PKC_PHOSPHO_SITE 79-81; 16-37,MYRISTYL 36-41; 1.092; CAMP_PHOSPHO_SITE 81-84; PKC_PHOSPHO_SITE 12-14;DEX0455_009.aa.1 N 1 - 189-217, MYRISTYL 335-340; MYRISTYL LAMP 1149-163; o1-328; 1.126; 83-88; PKC_PHOSPHO_SITE LYSASSOCTDMP tm329-351;139-145, 241-243; ASN_GLYCOSYLATION 139-163; i352-373; 1.097; 146-149;MYRISTYL 34-39; LYSASSOCTDMP 258-270, MYRISTYL 32-37; 267-281; 1.167;PKC_PHOSPHO_SITE 228-230; 38-61, AMIDATION 51-54; 1.154;PKC_PHOSPHO_SITE 4-6; 272-286, CK2_PHOSPHO_SITE 195-198; 1.083;ASN_GLYCOSYLATION 220-223; 156-177, PKC_PHOSPHO_SITE 13-15; 1.157;CK2_PHOSPHO_SITE 134-137; 73-122, 1.145; 231-240, 1.152; 289-321, 1.16;328-354, 1.187; 4-32, 1.238; 247-253, 1.064; DEX0455_010.orf.1 N 1 -51-57, MYRISTYL 57-62; MYRISTYL IG_LIKE 8-112; o1-109; 1.138; 52-57;MYRISTYL 140-145; IGc1 23-94; ig tm110-132; 78-98, 21-86; IG_MHCi133-148; 1.159; 82-88; 111-132, 1.193; 4-41, 1.243; 67-75, 1.122;DEX0455_010.aa.1 N 0 - 4-12, TYR_PHOSPHO_SITE 50-58;sp_P13761_HB2J_HUMAN o1-72; 1.148; CK2_PHOSPHO_SITE 37-40; 43-70; 34-44,PKC_PHOSPHO_SITE 37-39; 1.09; 55-69, 1.084; 22-28, 1.112;DEX0455_010.orf.2 Y 2 - 94-100, MYRISTYL 24-29; MYRISTYL IGc1 66-137; igo1-14; 1.138; 95-100; MYRISTYL 100-105; 64-129; IG_MHC tm15-37; 4-84,MYRISTYL 183-188; 125-131; i38-152; 1.243; IG_LIKE 51-155; tm153-175;154-175, o176-191; 1.193; 121-141, 1.159; 110-118, 1.122;DEX0455_010.aa.2 N 0 - 87-103, MYRISTYL 107-112; MYRISTYL IG_LIKE17-112; o1-112; 1.09; 61-66; MYRISTYL 66-71; IGc1 32-103; ig 60-66,CK2_PHOSPHO_SITE 106-109; 30-95; 1.138; MYRISTYL 96-101; 4-50, 1.243;76-84, 1.122; DEX0455_011.aa.1 N 0 - 78-97, PKC_PHOSPHO_SITE 82-84;GALAPTIN 61-81; o1-128; 1.118; ASN_GLYCOSYLATION 48-51; SUI1_1 115-122;99-115, CAMP_PHOSPHO_SITE 66-69; GLECT 4-128; 1.098; MYRISTYL 59-64;Gal-bind_lectin 7-33, ASN_GLYCOSYLATION 58-61; 1-128; 1.125;CK2_PHOSPHO_SITE 34-37; 37-43, 1.08; 118-125, 1.159; DEX0455_012.aa.1 N0 - 136-143, CK2_PHOSPHO_SITE 20-23; SAM_PNT 48-132; o1-256; 1.08;CK2_PHOSPHO_SITE 215-218; SAM_PNT 48-132; 193-199, MYRISTYL 202-207;1.037; CK2_PHOSPHO_SITE 132-135; 176-189, CK2_PHOSPHO_SITE 131-134;1.099; MYRISTYL 200-205; 69-82, CK2_PHOSPHO_SITE 93-96; 1.102; MYRISTYL53-58; 38-45, CK2_PHOSPHO_SITE 88-91; 1.131; MYRISTYL 182-187; 87-93,CAMP_PHOSPHO_SITE 237-240; 1.067; MYRISTYL 162-167; MYRISTYL 4-9, 1.066;249-254; PKC_PHOSPHO_SITE 100-128, 54-56; MYRISTYL 99-104; 1.153; 26-34,1.129; 236-245, 1.062; DEX0455_012.orf.2 N 0 - 4-10, 1.07;CK2_PHOSPHO_SITE 166-169; SAM_PNT 83-167; o1-250; 104-117, MYRISTYL 1-6;MYRISTYL SAM_PNT 83-167; 1.102; 134-139; MYRISTYL 217-222; 240-246,MYRISTYL 197-202; 1.107; CK2_PHOSPHO_SITE 167-170; 135-163, MYRISTYL88-93; 1.153; CK2_PHOSPHO_SITE 238-241; 16-32, PKC_PHOSPHO_SITE 89-91;1.09; CK2_PHOSPHO_SITE 128-131; 61-69, PKC_PHOSPHO_SITE 11-13; 1.129;MYRISTYL 28-33; MYRISTYL 228-234, 22-27; CK2_PHOSPHO_SITE 1.037;123-126; MYRISTYL 33-38; 73-80, MYRISTYL 235-240; 1.131;CK2_PHOSPHO_SITE 55-58; 122-128, 1.067; 171-178, 1.08; 37-44, 1.077;211-224, 1.099; DEX0455_012.aa.2 N 0 - 176-189, AMIDATION 273-276;ETSDOMAIN 330-348; o1-402; 1.099; MYRISTYL 53-58; AMIDATION ETSDOMAIN38-45, 377-380; CK2_PHOSPHO_SITE 349-367; 1.131; 246-249; MYRISTYL99-104; ETSDOMAIN 304-317; 288-294, CK2_PHOSPHO_SITE 224-227; SAM_PNT1.052; MYRISTYL 162-167; 48-132; AT_hook 26-34, CK2_PHOSPHO_SITE203-206; 275-287; 1.129; PKC_PHOSPHO_SITE 54-56; ETS_DOMAIN_3 69-82,ASN_GLYCOSYLATION 388-391; 304-386; 1.102; CK2_PHOSPHO_SITE 213-216;SAM_PNT 48-132; 205-218, CK2_PHOSPHO_SITE 88-91; HSF_ETS 314-376; 1.129;MYRISTYL 182-187; ETSDOMAIN 100-128, ASN_GLYCOSYLATION 354-357; 368-386;Ets 1.153; AMIDATION 293-296; 303-388; ETS 136-143, CK2_PHOSPHO_SITE20-23; 303-390; 1.08; CAMP_PHOSPHO_SITE 282-285; 311-318,CK2_PHOSPHO_SITE 93-96; 1.118; CAMP_PHOSPHO_SITE 350-353; 4-9, 1.066;CK2_PHOSPHO_SITE 132-135; 87-93, MYRISTYL 233-238; 1.067;CK2_PHOSPHO_SITE 131-134; 379-385, MYRISTYL 200-205; 1.088; 193-199,1.037; 332-346, 1.091; DEX0455_013.aa.1 N 0 - 38-45, CK2_PHOSPHO_SITE37-40; o1-219; 1.105; MYRISTYL 49-54; 183-198, ASN_GLYCOSYLATION 46-49;1.162; MYRISTYL 30-35; 129-146, CK2_PHOSPHO_SITE 173-176; 1.173;MYRISTYL 147-152; 154-173, PKC_PHOSPHO_SITE 200-202; 1.144; MYRISTYL100-105; 93-115, PKC_PHOSPHO_SITE 214-216; 1.187; 4-34, 1.161; 50-60,1.202; DEX0455_013.aa.2 N 0 - 82-99 CK2_PHOSPHO_SITE 126-129; o1-172;1.173; MYRISTYL 100-105; MYRISTYL 4-10, 53-58; PKC_PHOSPHO_SITE 1.154;167-169; PKC_PHOSPHO_SITE 46-68, 153-155; 1.187; 136-151, 1.162;107-126, 1.144; DEX0455_014.orf.1 N 0 - 4-10, CK2_PHOSPHO_SITE 110-113;EFh 204-232; o1-329; 1.104; CK2_PHOSPHO_SITE 24-27; EF_HAND_2_1 140-146,CAMP_PHOSPHO_SITE 198-201; 153-229; 1.062; PKC_PHOSPHO_SITE 95-97;EF_HAND 213-225; 76-82, PKC_PHOSPHO_SITE 308-310; Calpain III 1-133;1.057; CK2_PHOSPHO_SITE 156-159; EF_HAND 117-125, AMIDATION 12-15;243-255; efhand 1.126; CK2_PHOSPHO_SITE 177-180; 204-232; EFh 181-192,PKC_PHOSPHO_SITE 204-206; 234-262; 1.181; MYRISTYL 29-34; calpain_III5-133; 300-307, CK2_PHOSPHO_SITE 210-213; efhand 1.103; PKC_PHOSPHO_SITE126-128; 162-169, CK2_PHOSPHO_SITE 150-153; 234-262; 1.103;CK2_PHOSPHO_SITE 251-254; EF_HAND_2_2 314-320, PKC_PHOSPHO_SITE 24-26;237-294; 1.054; ASN_GLYCOSYLATION 299-302; 52-65, CK2_PHOSPHO_SITE22-25; 1.124; MYRISTYL 248-253; 197-212, 1.145; 235-242, 1.069; 32-40,1.209; 96-113, 1.1; 224-230, 1.049; 18-24, 1.096; 255-278, 1.221;290-298, 1.171; DEX0455_014.aa.1 N 0 - 21-44, CK2_PHOSPHO_SITE 153-156;Calpain_III o1-595; 1.113; ASN_GLYCOSYLATION 143-146; 261-399; 556-564,PKC_PHOSPHO_SITE 290-292; THIOL_PROTEASE_CYS 1.171; CK2_PHOSPHO_SITE200-203; 53-64; EFh 49-73, MYRISTYL 189-194; 470-498; 1.155;CK2_PHOSPHO_SITE 288-291; CALPAIN 89-114; 75-82, CK2_PHOSPHO_SITE290-293; efhand 500-528; 1.121; CK2_PHOSPHO_SITE 517-520; EF_HAND_2_1179-185, CK2_PHOSPHO_SITE 250-253; 419-495; 1.061; ASN_GLYCOSYLATION17-20; Peptidase_C2 284-290, MYRISTYL 295-300; 14-273; 1.096;PKC_PHOSPHO_SITE 392-394; CYS_PROT_CALPAIN 342-348, ASN_GLYCOSYLATION248-251; 32-273; CysPc 1.057; ASN_GLYCOSYLATION 565-568; 2-281; 117-125,PKC_PHOSPHO_SITE 252-254; EF_HAND_2_2 1.165; MYRISTYL 211-216; 503-560;103-110, CK2_PHOSPHO_SITE 221-224; CALPAIN 53-69; 1.113;CK2_PHOSPHO_SITE 422-425; EFh 500-528; 566-573, CAMP_PHOSPHO_SITE464-467; EF_HAND 509-521; 1.103; MYRISTYL 164-169; MYRISTYL CALPAIN259-275, 144-149; CK2_PHOSPHO_SITE 29-51; EF_HAND 1.108; 114-117;CK2_PHOSPHO_SITE 479-491; 428-435, 47-50; PKC_PHOSPHO_SITE calpain_III1.103; 114-116; MYRISTYL 45-50; 241-399; 188-197, PKC_PHOSPHO_SITE470-472; CALPAIN 365-393; 1.149; PKC_PHOSPHO_SITE 227-229; efhand 86-98,CK2_PHOSPHO_SITE 19-22; 470-498; 1.077; PKC_PHOSPHO_SITE 361-363;CALPAIN 119-142; 318-331, CK2_PHOSPHO_SITE 376-379; 1.124;CK2_PHOSPHO_SITE 476-479; 447-458, MYRISTYL 514-519; 1.181;PKC_PHOSPHO_SITE 574-576; 132-143, CK2_PHOSPHO_SITE 443-446; 1.081;CK2_PHOSPHO_SITE 416-419; 4-11, CAMP_PHOSPHO_SITE 187-190; 1.247;TYR_PHOSPHO_SITE 172-179; 362-379, 1.1; 209-229, 1.083; 490-496, 1.049;298-306, 1.209; 521-544, 1.221; 580-586, 1.054; 463-478, 1.145; 501-508,1.069; 383-391, 1.126; 406-412, 1.062; DEX0455_015.aa.1 N 0 - 63-82,CK2_PHOSPHO_SITE 42-45; ER_TARGET 82-85; o1-85; 1.15; PKC_PHOSPHO_SITE35-37; 20-26, CK2_PHOSPHO_SITE 81-84; 1.04; CK2_PHOSPHO_SITE 19-22;4-14, PKC_PHOSPHO_SITE 68-70; 1.174; 35-46, 1.138; DEX0455_016.aa.1 N0 - 105-110, MYRISTYL 24-29; MYRISTYL KH 189-240; o1-255; 1.047; 22-27;PKC_PHOSPHO_SITE GLY_RICH 13-26; 223-241, 207-209; MYRISTYL 152-157; KH99-169; KH 1.155; MYRISTYL 21-26; MYRISTYL 184-239; 75-81, 225-230;MYRISTYL 198-203; KH_TYPE_1_1 1.064; MYRISTYL 16-21; MYRISTYL 100-164;KH 244-252, 17-22; MYRISTYL 18-23; 104-152; 1.167; ASN_GLYCOSYLATION82-85; KH_TYPE_1_2 86-94, MYRISTYL 13-18; MYRISTYL 185-224; 1.048;20-25; MYRISTYL 46-51; 145-151, MYRISTYL 26-31; MYRISTYL 1.048; 19-24;MYRISTYL 50-55; 154-171, PKC_PHOSPHO_SITE 159-161; 1.113; 185-202,1.095; 4-12, 1.094; 32-44, 1.04; 129-138, 1.113; DEX0455_017.aa.1 N 0 -82-95, ASN_GLYCOSYLATION 29-32; TM4_2 16-124; o1-174; 1.136; MYRISTYL104-109; 112-129, PKC_PHOSPHO_SITE 166-168; 1.149; ASN_GLYCOSYLATION42-45; 98-110, PKC_PHOSPHO_SITE 162-164; 1.124; CK2_PHOSPHO_SITE 70-73;58-65, PKC_PHOSPHO_SITE 31-33; 1.171; ASN_GLYCOSYLATION 72-75; 138-155,MYRISTYL 105-110; 1.209; CK2_PHOSPHO_SITE 44-47; 4-15, MYRISTYL 34-39;MYRISTYL 1.221; 112-117; ASN_GLYCOSYLATION 34-41, 66-69;CK2_PHOSPHO_SITE 1.125; 20-23; DEX0455_018.aa.1 N 0 - 152-174, MYRISTYL174-179; PROTEIN_KINASE_DOM o1-354; 1.101; CK2_PHOSPHO_SITE 62-65;10-283; 232-240, PKC_PHOSPHO_SITE 334-336; TYRKINASE 104-117; 1.163;PKC_PHOSPHO_SITE 348-350; S_TK_X 67-74, CK2_PHOSPHO_SITE 11-14; 284-348;1.098; MYRISTYL 319-324; sp_Q9UM03_Q9UM03_HUMAN 289-311,PKC_PHOSPHO_SITE 46-48; 37-283; 1.168; CK2_PHOSPHO_SITE 228-231; S_TKc37—283; 57-63, MYRISTYL 19-24; MYRISTYL TyrKc 38-277; 1.087; 18-23;TYR_PHOSPHO_SITE PROTEIN_KINASE_ST 33-44, 63-70; 145-157; 1.198;TYRKINASE 139-157; 207-225, TYRKINASE 1.149; 205-227; 276-282, pkinase_C284-351; 1.104; pkinase 22-28, 31-283; 1.058; 117-150, 1.291; 243-265,1.125; 319-338, 1.116; 182-199, 1.136; 344-350, 1.079; 49-55, 1.112;76-110, 1.213; DEX0455_018.aa.2 N 0 - 356-363, CK2_PHOSPHO_SITE 135-138;HR1 105-181; o1-489; 1.123; PKC_PHOSPHO_SITE 60-62; HR1 182-255;215-226, PKC_PHOSPHO_SITE 434-436; HR1 18-90; HR1 1.053;PKC_PHOSPHO_SITE 206-208; 18-90; 151-169, MYRISTYL 442-447; REM_REPEAT_11.163; PKC_PHOSPHO_SITE 45-47; 15-74; HR1 182-255; 175-195,CK2_PHOSPHO_SITE 307-310; REM_REPEAT_2 1.157; PKC_PHOSPHO_SITE 453-455;107-166; HR1 378-390, LEUCINE_ZIPPER 50-71; 105-181; 1.189;PKC_PHOSPHO_SITE 205-207; REM_REPEAT_3 103-122, CK2_PHOSPHO_SITE164-167; 175-239; 1.165; LEUCINE_ZIPPER 222-243; 50-59,ASN_GLYCOSYLATION 126-129; 1.127; MYRISTYL 452-457; 258-276,CK2_PHOSPHO_SITE 414-417; 1.096; MYRISTYL 407-412; 228-252,PKC_PHOSPHO_SITE 226-228; 1.133; PKC_PHOSPHO_SITE 135-137; 129-134,LEUCINE_ZIPPER 215-236; 1.041; 393-422, 1.174; 440-457, 1.171; 459-483,1.218; 327-343, 1.235; 139-147, 1.103; 278-307, 1.151; 88-94, 1.072;65-83, 1.135; 198-206, 1.174; DEX0455_019.aa.1 Y 0 - 209-234, MYRISTYL82-87; AMIDATION Folate_rec 7-287; o1-287; 1.163; 102-105; MYRISTYL214-219; 268-274, PKC_PHOSPHO_SITE 26-28; 1.108; ASN_GLYCOSYLATION243-246; 249-254, ASN_GLYCOSYLATION 163-166; 1.037; PKC_PHOSPHO_SITE238-240; 171-180, PKC_PHOSPHO_SITE 193-195; 1.184; MYRISTYL 247-252;65-73, CK2_PHOSPHO_SITE 218-221; 1.106; PKC_PHOSPHO_SITE 165-167;189-197, ASN_GLYCOSYLATION 203-206; 1.098; CK2_PHOSPHO_SITE 48-51; 8-21,PKC_PHOSPHO_SITE 248-250; 1.242; 91-102, 1.114; 54-60, 1.089; 129-136,1.123; 33-40, 1.121; 236-244, 1.078; 109-127, 1.096; 140-154, 1.114;DEX0455_020.aa.1 N 0 - 73-79, AMIDATION 25-28; o1-143; 1.044;CK2_PHOSPHO_SITE 99-102; 101-120, MYRISTYL 126-131; MYRISTYL 1.206;79-84; PKC_PHOSPHO_SITE 129-140, 71-73; MYRISTYL 119-124; 1.111;MYRISTYL 75-80; 27-32, PKC_PHOSPHO_SITE 72-74; 1.039; ASN_GLYCOSYLATION97-100; 83-93, PKC_PHOSPHO_SITE 136-138; 1.128; MYRISTYL 68-73; 4-18,1.179; 46-67, 1.134; DEX0455_020.orf.2 N 0 - 32-64, MYRISTYL 106-111;o1-116; 1.153; CK2_PHOSPHO_SITE 34-37; 84-90, PKC_PHOSPHO_SITE 12-14;1.128; MYRISTYL 6-11; MYRISTYL 96-102, 29-34; MYRISTYL 68-73; 1.085;AMIDATION 61-64; 13-21, PKC_PHOSPHO_SITE 78-80; 1.109; MYRISTYL 92-97;CK2_PHOSPHO_SITE 25-28; DEX0455_020.aa.2 N 0 - 29-46, CK2_PHOSPHO_SITE44-47; o1-67; 1.092; ASN_GLYCOSYLATION 25-28; 52-64, MYRISTYL 7-12;1.187; 11-21, 1.128; DEX0455_021.orf.1 N 0 - 86-97, PKC_PHOSPHO_SITE81-83; o1-104; 1.124; PKC_PHOSPHO_SITE 100-102; 4-9, 1.11;CAMP_PHOSPHO_SITE 33-36; 35-71, PKC_PHOSPHO_SITE 32-34; 1.171; MYRISTYL10-15; 14-22, 1.095; DEX0455_021.aa.1 N 0 - 45-51, o1-82; 1.09; 4-11,1.131; 15-23, 1.096; DEX0455_021.aa.2 N 0 - 112-119, ASN_GLYCOSYLATION108-111; Epimerase 5-311; o1-360; 1.083; MYRISTYL 203-208; galE 4-296;209-218, AMIDATION 217-220; 1.167; CK2_PHOSPHO_SITE 44-47; 121-147,AMIDATION 325-328; 1.118; PKC_PHOSPHO_SITE 48-50; 179-186,CK2_PHOSPHO_SITE 18-21; 1.153; CAMP_PHOSPHO_SITE 78-81; 73-108,PKC_PHOSPHO_SITE 56-58; 1.131; MYRISTYL 263-268; MYRISTYL 290-300,190-195; 1.12; 169-175, 1.09; 46-55, 1.071; 309-318, 1.162; 4-10, 1.11;341-347, 1.071; 13-34, 1.181; 193-199, 1.098; 239-267, 1.186;DEX0455_021.orf.3 N 0 - 24-47, CK2_PHOSPHO_SITE 92-95; galE 52-344;o1-376; 1.119; MYRISTYL 4-9; Epimerase 53-359; 241-247, PKC_PHOSPHO_SITE96-98; 1.098; MYRISTYL 8-13; 94-103, PKC_PHOSPHO_SITE 104-106; 1.071;CAMP_PHOSPHO_SITE 126-129; 61-82, MYRISTYL 238-243; 1.181;CK2_PHOSPHO_SITE 66-69; 357-366, MYRISTYL 9-14; AMIDATION 1.162;373-376; MYRISTYL 6-11; 51-58, MYRISTYL 10-15; 1.11; ASN_GLYCOSYLATION156-159; 257-266, AMIDATION 265-268; 1.167; MYRISTYL 311-316; MYRISTYL169-195, 251-256; 1.118; 121-156, 1.131; 160-167, 1.083; 287-315, 1.186;338-348, 1.12; 217-223, 1.09; 227-234, 1.153; DEX0455_021.aa.3 N 0 -290-300, PKC_PHOSPHO_SITE 48-50; galE 4-462; o1-466; 1.12; MYRISTYL203-208; Epimerase 5-459; 239-267, AMIDATION 217-220; 1.186;PKC_PHOSPHO_SITE 56-58; 209-218, MYRISTYL 263-268; 1.167; AMIDATION325-328; 399-417, PKC_PHOSPHO_SITE 399-401; 1.182; PKC_PHOSPHO_SITE372-374; 193-199, MYRISTYL 359-364; MYRISTYL 1.098; 190-195;ASN_GLYCOSYLATION 4-10, 1.11; 108-111; PKC_PHOSPHO_SITE 121-147,346-348; CK2_PHOSPHO_SITE 1.118; 44-47; CAMP_PHOSPHO_SITE 46-55, 78-81;CK2_PHOSPHO_SITE 1.071; 18-21; 112-119, 1.083; 337-393, 1.213; 13-34,1.181; 309-318, 1.162; 73-108, 1.131; 169-175, 1.09; 422-434, 1.145;179-186, 1.153; DEX0455_021.aa.4 N 0 - 112-119, MYRISTYL 190-195;MYRISTYL galE 4-296; o1-328; 1.083; 263-268; PKC_PHOSPHO_SITE Epimerase5-311; 239-267, 56-58; CK2_PHOSPHO_SITE 1.186; 44-47; MYRISTYL 203-208;193-199, CK2_PHOSPHO_SITE 18-21; 1.098; AMIDATION 217-220; 169-175,ASN_GLYCOSYLATION 108-111; 1.09; PKC_PHOSPHO_SITE 48-50; 309-318,AMIDATION 325-328; 1.162; CAMP_PHOSPHO_SITE 78-81; 73-108, 1.131;209-218, 1.167; 290-300, 1.12; 121-147, 1.118; 13-34, 1.181; 46-55,1.071; 179-186, 1.153; 4-10, 1.11; DEX0455_022.aa.1 Y 1 - 54-73,PKC_PHOSPHO_SITE 145-147; i1-21; 1.132; TYR_PHOSPHO_SITE 147-154;tm22-44; 19-46, AMIDATION 173-176; o45-178; 1.26; CK2_PHOSPHO_SITE 4-7;123-135, ASN_GLYCOSYLATION 65-68; 1.041; ASN_GLYCOSYLATION 92-95; 5-12,PKC_PHOSPHO_SITE 45-47; 1.131; CK2_PHOSPHO_SITE 156-159; 81-101, 1.08;140-149, 1.16; 151-157, 1.051; 161-171, 1.056; DEX0455_022.orf.2 Y 1 -32-59, ASN_GLYCOSYLATION 78-81; o1-34; 1.26; PKC_PHOSPHO_SITE 58-60;tm35-57; 67-86, PKC_PHOSPHO_SITE 7-9; i58-141; 1.132; CK2_PHOSPHO_SITE17-20; 4-9, 1.102; ASN_GLYCOSYLATION 105-108; 126-138, 1.071; 18-25,1.131; 94-114, 1.08; DEX0455_022.aa.2 Y 1 - 113-128, ASN_GLYCOSYLATION92-95; i1-21; 1.071; ASN_GLYCOSYLATION 65-68; tm22-44; 131-144,TYR_PHOSPHO_SITE 155-162; o45-188; 1.136; PKC_PHOSPHO_SITE 153-155;148-157, CK2_PHOSPHO_SITE 4-7; 1.16; PKC_PHOSPHO_SITE 45-47; 19-46,CK2_PHOSPHO_SITE 164-167; 1.26; 81-101, 1.08; 5-12, 1.131 169-185,1.221; 159-165, 1.051; 54-73, 1.132; DEX0455_022.aa.3 Y 0 - 6-14, 1.07;MYRISTYL 48-53; MYRISTYL GLY_RICH 5-48; o1-78; 48-65, 34-39; MYRISTYL14-19; 1.202; MYRISTYL 27-32; MYRISTYL 70-75, 6-11; PKC_PHOSPHO_SITE68-70; 1.085; MYRISTYL 39-44; MYRISTYL 13-18; MYRISTYL 20-25;DEX0455_023.aa.1 N 0 - 69-80, PKC_PHOSPHO_SITE 57-59; o1-116; 1.147;CAMP_PHOSPHO_SITE 48-51; 50-61, PKC_PHOSPHO_SITE 52-54; 1.08;PKC_PHOSPHO_SITE 47-49; 27-37, PKC_PHOSPHO_SITE 101-103; 1.085;PKC_PHOSPHO_SITE 43-45; 82-89, CK2_PHOSPHO_SITE 36-39; 1.049; AMIDATION39-42; 4-13, 1.11; PKC_PHOSPHO_SITE 97-99; CAMP_PHOSPHO_SITE 54-57;DEX0455_024.aa.1 N 0 - 245-252, PKC_PHOSPHO_SITE 34-36; ANNEXINI343-356; o1-360; 1.15; PKC_PHOSPHO_SITE 257-259; sp_P09525_ANX4_HUMAN127-136, PKC_PHOSPHO_SITE 33-35; 131-196; 1.145; PKC_PHOSPHO_SITE298-300; ANNEXINV 219-245; 208-215, MYRISTYL 6-11; MYRISTYL annexin1.12; 144-149; CK2_PHOSPHO_SITE 212-280; 309-317, 176-179;ASN_GLYCOSYLATION ANNEXINV 343-356; 1.126; 286-289; PKC_PHOSPHO_SITEANNEXINV 117-124, 22-24; CAMP_PHOSPHO_SITE 136-157; 1.107; 254-257;MYRISTYL 29-34; annexin 288-355; 274-284, PKC_PHOSPHO_SITE 7-9; ANNEXIN1.206; CK2_PHOSPHO_SITE 344-347; 109-125; 189-197, CK2_PHOSPHO_SITE315-318; sp_P08132_ANX4_PIG 1.193; CK2_PHOSPHO_SITE 272-275; 214-283;348-357, CAMP_PHOSPHO_SITE 163-166; ANNEXIN 136-157; 1.265;CK2_PHOSPHO_SITE 71-74; sp_Q9NFS4_Q9NFS4_GIALA 324-340, MYRISTYL303-308; 89-348; 1.091; CK2_PHOSPHO_SITE 158-161; ANNEXIN 219-245;147-157, PKC_PHOSPHO_SITE 264-266; ANNEXINV 1.162; CK2_PHOSPHO_SITE73-76; 299-325; 78-85, CK2_PHOSPHO_SITE 257-260; ANNEXIN 72-124; 1.168;ANNEXINI 299-319; 232-240, ANNEXINI 1.187; 219-245; 167-172, annexin16-124; 1.042; ANNEXIN 228-280; 289-295, ANNEXINI 1.073; 136-157; 61-70,annexin 129-196; 1.189; ANX 303-355; ANNEXINV 69-91; ANX 144-196;ANNEXINI 69-91; ANNEXINI 109-125; ANNEXIN 69-91; sp_P09525_ANX4_HUMAN290-358; ANX 228-280; ANNEXINV 109-125; ANX 72-124; ANNEXIN 303-355;ANNEXINI 109-125; ANNEXINII 136-157; ANNEXINII 69-91; ANNEXINII 343-356;ANNEXIN 144-196; ANNEXINII 299-319; sp_P09525_ANX4_HUMAN 63-127; ANNEXIN299-319; ANNEXINII 219-245; ANNEXIN 343-356; DEX0455_024.aa.2 N 0 -4-14, CK2_PHOSPHO_SITE 132-135; ANNEXINIV 36-62; o1-177; 1.157;CK2_PHOSPHO_SITE 161-164; sp_P08132_ANX4_PIG 165-174, ASN_GLYCOSYLATION103-106; 31-100; 1.265; MYRISTYL 120-125; ANNEXINII 36-62; 141-157,CK2_PHOSPHO_SITE 89-92; sp_P09525_ANX4_HUMAN 1.091; CAMP_PHOSPHO_SITE71-74; 107-175; 91-101, PKC_PHOSPHO_SITE 115-117; ANNEXINII 160-173;1.206; PKC_PHOSPHO_SITE 81-83; ANNEXINII 126-134, PKC_PHOSPHO_SITE74-76; 116-136; 1.126; CK2_PHOSPHO_SITE 74-77; ANNEXIN 160-173; 49-57,ANNEXINIV 1.187; 160-173; 25-32, annexin 29-97; 1.12; ANNEXIN 120-172;106-112, ANX 45-97; 1.073; ANNEXIN 36-62; 62-69, ANX 120-172; 1.15;ANNEXIN 45-97; ANNEXINIV 116-142; ANNEXIN 116-136; annexin 105-172;DEX0455_025.aa.1 N 0 - 55-61, PKC_PHOSPHO_SITE 296-298; o1-380; 1.085;CK2_PHOSPHO_SITE 230-233; 95-102, MYRISTYL 357-362; 1.121;CK2_PHOSPHO_SITE 118-121; 124-165, TYR_PHOSPHO_SITE 298-305; 1.203;ASN_GLYCOSYLATION 51-54; 253-265, PKC_PHOSPHO_SITE 358-360; 1.112;CK2_PHOSPHO_SITE 318-321; 280-315, ASN_GLYCOSYLATION 344-347; 1.154;MYRISTYL 55-60; 201-211, PKC_PHOSPHO_SITE 349-351; 1.092; MYRISTYL224-229; 323-341, CK2_PHOSPHO_SITE 169-172; 1.121; PKC_PHOSPHO_SITE71-73; 25-49, CK2_PHOSPHO_SITE 352-355; 1.169; CK2_PHOSPHO_SITE 308-311;350-357; CK2_PHOSPHO_SITE 228-231; 1.074; PKC_PHOSPHO_SITE 68-70;362-370, 1.179; 9-15, 1.13; 269-278, 1.061; 73-90, 1.133; 175-185,1.225; 243-250, 1.061; 111-121, 1.127; DEX0455_025.orf.2 Y 0 - 329-364,PKC_PHOSPHO_SITE 45-47; o1-394; 1.154; CK2_PHOSPHO_SITE 35-38; 318-327,TYR_PHOSPHO_SITE 347-354; 1.061; MYRISTYL 104-109; 18-31,PKC_PHOSPHO_SITE 117-119; 1.139; PKC_PHOSPHO_SITE 120-122; 4-15, 1.18;CK2_PHOSPHO_SITE 357-360; 104-110, CK2_PHOSPHO_SITE 218-221; 1.085;PKC_PHOSPHO_SITE 15-17; 122-139, CK2_PHOSPHO_SITE 279-282; 1.133;MYRISTYL 273-278; 302-314, CK2_PHOSPHO_SITE 277-280; 1.112;ASN_GLYCOSYLATION 100-103; 250-260, CK2_PHOSPHO_SITE 15-18; 1.092;PKC_PHOSPHO_SITE 345-347; 74-98, CK2_PHOSPHO_SITE 367-370; 1.169;CK2_PHOSPHO_SITE 167-170; 372-391, 1.121; 292-299, 1.061; 173-214,1.203; 36-43, 1.073; 160-170, 1.127; 144-151, 1.121; 224-234, 1.225;58-64, 1.13; DEX0455_025.aa.2 N 0 - 95-102, PKC_PHOSPHO_SITE 652-654;o1-679; 1.121; PKC_PHOSPHO_SITE 296-298; 557-564, TYR_PHOSPHO_SITE298-305; 1.066; MYRISTYL 224-229; 111-121, PKC_PHOSPHO_SITE 632-634;1.127; CK2_PHOSPHO_SITE 653-656; 9-15, 1.13; CK2_PHOSPHO_SITE 228-231;655-665, MYRISTYL 349-354; 1.082; CK2_PHOSPHO_SITE 230-233; 243-250,MYRISTYL 507-512; MYRISTYL 1.061; 361-366; PKC_PHOSPHO_SITE 73-90,588-590; CK2_PHOSPHO_SITE 1.133; 640-643; PKC_PHOSPHO_SITE 507-513,526-528; MYRISTYL 55-60; 1.056; PKC_PHOSPHO_SITE 555-557; 124-165,CK2_PHOSPHO_SITE 118-121; 1.203; PKC_PHOSPHO_SITE 71-73; 539-548,LEUCINE_ZIPPER 453-474; 1.107; PKC_PHOSPHO_SITE 631-633; 623-630,PKC_PHOSPHO_SITE 68-70; 1.089; CK2_PHOSPHO_SITE 540-543; 253-265,PKC_PHOSPHO_SITE 513-515; 1.112; ASN_GLYCOSYLATION 51-54; 360-365,MYRISTYL 674-679; 1.048; CK2_PHOSPHO_SITE 318-321; 280-315,CK2_PHOSPHO_SITE 308-311; 1.154; CK2_PHOSPHO_SITE 169-172; 386-392,1.069; 394-416, 1.152; 489-499, 1.139; 269-278, 1.061; 368-384, 1.143;578-589, 1.155; 175-185, 1.225; 473-482, 1.179; 201-211, 1.092; 323-355,1.122; 25-49, 1.169; 424-465, 1.143; 55-61, 1.085; 633-639, 1.052;601-618, 1.106; 521-528, 1.118; DEX0455_026.orf.1 N 0 -ASN_GLYCOSYLATION 46-49; i1-72; CK2_PHOSPHO_SITE 62-65; DEX0455_026.aa.1N 0 - 69-74, CK2_PHOSPHO_SITE 58-61; i1-77; 1.113; CK2_PHOSPHO_SITE53-56; 47-54, 1.103; 7-34, 1.196; DEX0455_027.orf.1 N 0 - 54-76,CK2_PHOSPHO_SITE 65-68; o1-174; 1.16; MYRISTYL 53-58; MYRISTYL 118-139,40-45; PKC_PHOSPHO_SITE 1.134; 75-77; ASN_GLYCOSYLATION 40-52, 93-96;CK2_PHOSPHO_SITE 1.162; 171-174; CK2_PHOSPHO_SITE 4-20, 114-117;CK2_PHOSPHO_SITE 1.164; 83-86; MYRISTYL 152-157; 155-171, 1.137;103-113, 1.167; DEX0455_027.aa.1 N 0 - 5-28, i1-36; 1.145;DEX0455_028.aa.1 N 0 - MYRISTYL 144-149; cobW 41-214; o1-215;CK2_PHOSPHO_SITE 30-33; ATP_GTP_A 49-56; PKC_PHOSPHO_SITE 111-113;PKC_PHOSPHO_SITE 68-70; CK2_PHOSPHO_SITE 111-114; MYRISTYL 52-57;CK2_PHOSPHO_SITE 167-170; CK2_PHOSPHO_SITE 28-31; GLYCOSAMINOGLYCAN36-39; MYRISTYL 106-111; CK2_PHOSPHO_SITE 7-10; PKC_PHOSPHO_SITE210-212; CK2_PHOSPHO_SITE 82-85; DEX0455_029.orf.1 Y 0 - 109-124,CK2_PHOSPHO_SITE 120-123; o1-133; 1.141; 4-18, 1.154; 26-79, 1.144;DEX0455_029.aa.1 N 5 - 589-601, CK2_PHOSPHO_SITE 503-506; i1-20; 1.168;PKC_PHOSPHO_SITE 546-548; tm21-43; 141-213, CK2_PHOSPHO_SITE 714-717;o44-55; 1.251; ASN_GLYCOSYLATION 747-750; tm56-78; 4-19, MYRISTYL695-700; i79-188; 1.116; PKC_PHOSPHO_SITE 716-718; tm189-211; 84-92,ASN_GLYCOSYLATION 51-54; o212-265; 1.108; MYRISTYL 651-656; tm266-288;810-816, PKC_PHOSPHO_SITE 351-353; i289-294; 1.062; ASN_GLYCOSYLATION228-231; tm295-317; 787-805, CK2_PHOSPHO_SITE 697-700; o318-953; 1.18;PKC_PHOSPHO_SITE 808-810; 292-319, ASN_GLYCOSYLATION 782-785; 1.22;CK2_PHOSPHO_SITE 904-907; 818-881, PKC_PHOSPHO_SITE 622-624; 1.176;PKC_PHOSPHO_SITE 904-906; 914-920, TYR_PHOSPHO_SITE 297-303; 1.094;PKC_PHOSPHO_SITE 755-757; 121-132, PKC_PHOSPHO_SITE 784-786; 1.185;PKC_PHOSPHO_SITE 317-319; 721-739, PKC_PHOSPHO_SITE 2-4; 1.162;PKC_PHOSPHO_SITE 879-881; 531-544, CK2_PHOSPHO_SITE 546-549; 1.196;PKC_PHOSPHO_SITE 332-334; 655-680, PKC_PHOSPHO_SITE 835-837; 1.23;MYRISTYL 130-135; 52-80, CK2_PHOSPHO_SITE 936-939; 1.244;PKC_PHOSPHO_SITE 139-141; 348-380, CK2_PHOSPHO_SITE 934-937; 1.166;ASN_GLYCOSYLATION 741-744; 388-401, PKC_PHOSPHO_SITE 259-261; 1.1;PKC_PHOSPHO_SITE 938-940; 700-708, CK2_PHOSPHO_SITE 879-882; 1.061;PKC_PHOSPHO_SITE 230-232; 609-619, PKC_PHOSPHO_SITE 912-914; 1.166;MYRISTYL 240-245; 753-782, PKC_PHOSPHO_SITE 909-911; 1.251;PKC_PHOSPHO_SITE 161-163; 321-340, 1.148; 551-568, 1.095; 884-898,1.185; 570-587, 1.245; 924-935, 1.123; 691-697, 1.081; 255-286, 1.151;409-462, 1.144; 99-116, 1.162; 492-507, 1.141; 21-46, 1.201; 243-252,1.116; 512-524, 1.154; 624-652, 1.188; DEX0455_029.orf.2 Y 0 - 26-79,CK2_PHOSPHO_SITE 145-148; cobW 1-176; o1-194; 1.144; PKC_PHOSPHO_SITE153-155; 165-176, PKC_PHOSPHO_SITE 145-147; 1.123; PKC_PHOSPHO_SITE120-122; 125-139, PKC_PHOSPHO_SITE 179-181; 1.185; CK2_PHOSPHO_SITE177-180; 109-122, PKC_PHOSPHO_SITE 150-152; 1.122; CK2_PHOSPHO_SITE120-123; 4-18, CK2_PHOSPHO_SITE 175-178; 1.154; 155-161, 1.094;DEX0455_029.aa.2 N 6 - 499-531, PKC_PHOSPHO_SITE 312-314; cobW 458-710;o1-129; 1.166; TYR_PHOSPHO_SITE 448-454; tm130-149; 154-160,PKC_PHOSPHO_SITE 290-292; i150-168; 1.051; PKC_PHOSPHO_SITE 381-383;tm169-191; 9-27, PKC_PHOSPHO_SITE 410-412; o192-205; 1.196;CK2_PHOSPHO_SITE 32-35; tm206-228; 689-695, CK2_PHOSPHO_SITE 709-712;i229-339; 1.094; PKC_PHOSPHO_SITE 654-656; tm340-362; 94-120,CK2_PHOSPHO_SITE 654-657; o363-416; 1.182; ASN_GLYCOSYLATION 379-382;tm417-439; 560-613, ASN_GLYCOSYLATION 202-205; i440-445; 1.144;PKC_PHOSPHO_SITE 4-6; tm446-468; 250-283, CK2_PHOSPHO_SITE 113-116;o469-728; 1.185; MYRISTYL 391-396; 406-437, PKC_PHOSPHO_SITE 153-155;1.151; PKC_PHOSPHO_SITE 713-715; 472-491, PKC_PHOSPHO_SITE 687-689;1.148; PKC_PHOSPHO_SITE 684-686; 699-710, CK2_PHOSPHO_SITE 711-714;1.123; PKC_PHOSPHO_SITE 468-470; 172-197, PKC_PHOSPHO_SITE 90-92; 1.201;ASN_GLYCOSYLATION 120-123; 162-170, PKC_PHOSPHO_SITE 502-504; 1.116;MYRISTYL 281-286; 292-364, CK2_PHOSPHO_SITE 679-682; 1.251;PKC_PHOSPHO_SITE 483-485; 538-552, PKC_PHOSPHO_SITE 679-681; 1.1;659-673, 1.185; 394-403, 1.116; 38-69, 1.174; 443-470, 1.22; 126-152,1.243; 74-83, 1.196; 643-656, 1.122; 203-243, 1.244;DEX0455_0455_030.aa.1 N 0 - 250-278, CK2_PHOSPHO_SITE 5-8; Metallophos47-242; o1-312; 1.145; MYRISTYL 267-272; STPHPHTASE 42-55,PKC_PHOSPHO_SITE 209-211; 48-75; 1.148; ASN_GLYCOSYLATION 250-253;STPHPHTASE 145-171; 185-198, CK2_PHOSPHO_SITE 198-201; STPHPHTASE 1.08;MYRISTYL 166-171; MYRISTYL 230-250; 22-40, 113-118; TYR_PHOSPHO_SITESTPHPHTASE 252-268; 1.148; 141-149; STPHPHTASE 213-225, 77-104; PP2Ac1.123; 20-290; 57-71, STPHPHTASE 174-201; 1.09; PHOSPHO_ESTER 120-175,47-245; 1.145; STPHPHTASE 110-134; 10-20, sp_P33172_PPP4_HUMAN 1.094;7-290; 299-309, SER_THR_PHOSPHATASE 1.17; 111-116; 232-243, 1.157;280-289, 1.066; 85-105, 1.201; DEX0455_030.aa.2 N 0 - 108-118,PKC_PHOSPHO_SITE 126-128; STPHPHTASE 169-182; o1-182; 1.128;PKC_PHOSPHO_SITE 95-97; sp_P11084_PPP4_RABIT 4-12, CK2_PHOSPHO_SITE53-56; 104-182; 1.114; CK2_PHOSPHO_SITE 116-119; STPHPHTASE 147-167;47-67, MYRISTYL 83-88; PP2Ac 33-182; 1.252; ASN_GLYCOSYLATION 167-170;71-81, 1.118; 38-44, 1.1; 149-160, 1.157; 91-97, 1.075; 167-179, 1.128;18-36, 1.164; 130-142, 1.123; DEX0455_031.orf.1 Y 0 - 161-189,ASN_GLYCOSYLATION 78-81; TNFR_NGFR_1 o1-293; 1.17; MYRISTYL 103-108;121-164; 150-156, CK2_PHOSPHO_SITE 80-83; TNFR_c6 81-118; 1.092;MYRISTYL 233-238; TNFR_NGFR_2_2 285-190, PKC_PHOSPHO_SITE 220-222;120-162; 1.091; MYRISTYL 167-172; MYRISTYL CYS_RICH 96-186; 12-45,201-206; CK2_PHOSPHO_SITE TNFR 81-118; 1.129; 178-181; PKC_PHOSPHO_SITETNFR_c6 89-124, 10-12; MYRISTYL 281-286; 208-248; 1.191; MYRISTYL 61-66;AMIDATION TNFR_NGFR_2_3 249-255, 16-19; PKC_PHOSPHO_SITE 207-248; 1.087;247-249; PKC_PHOSPHO_SITE TNFR_NGFR_1 81-118; 203-211, 156-158;CK2_PHOSPHO_SITE TNFR 121-162; 1.196; 125-128; CAMP_PHOSPHO_SITE TNFR164-205; 231-238, 157-160; PKC_PHOSPHO_SITE TNFR_c6 1.08; 80-82;PKC_PHOSPHO_SITE 121-162; TNFR 47-74, 107-109; PKC_PHOSPHO_SITE 208-248;1.166; 155-157; CK2_PHOSPHO_SITE TNFR_c6 164-194; 262-279, 120-123;MYRISTYL 240-245; TNFR_NGFR_2_1 1.144; CAMP_PHOSPHO_SITE 18-21; 194;80-118; 220-227, TYR_PHOSPHO_SITE 82-89; 1.113; CK2_PHOSPHO_SITE227-230; 132-148, CK2_PHOSPHO_SITE 190-193; 1.205; ASN_GLYCOSYLATION215-218; DEX0455_031.aa.1 Y 1 - 193-200, MYRISTYL 23-28; TNFR_NGFR_143-80; o1-425; 1.08; PKC_PHOSPHO_SITE 182-184; TNFR_NGFR_2_3 tm426-448;51-86, PKC_PHOSPHO_SITE 331-333; 169-210; i449-635; 1.191;TYR_PHOSPHO_SITE 44-51; TNFR_c6 43-80; 165-173, ASN_GLYCOSYLATION177-180; CYS_RICH 58-148; 1.196; CK2_PHOSPHO_SITE 523-526; PRO_RICH614-621, MYRISTYL 547-552; 567-602; 1.063; PKC_PHOSPHO_SITE 209-211;TNFR_NGFR_2_2 182-189, MYRISTYL 65-70; MYRISTYL 82-124; 1.113; 552-557;PKC_PHOSPHO_SITE TNFR_NGFR_1 83-126; 427-464, 118-120; AMIDATION382-385; TNFR 43-80; 1.216; MYRISTYL 195-200; TNFR_NGFR_2_1 112-118,CK2_PHOSPHO_SITE 87-90; 42-80; TNFR 83-124; 1.092; PKC_PHOSPHO_SITE623-625; TNFR_c6 268-294, MYRISTYL 202-207; MYRISTYL 83-124; TNFR 1.175;411-416; MYRISTYL 376-381; 126-167; 211-217, MYRISTYL 286-291; TNFR_c6170-210; 1.087; CAMP_PHOSPHO_SITE 119-122; TNFR 170-210; 344-423,MYRISTYL 396-401; TNFR_c6 1.224; CK2_PHOSPHO_SITE 140-143; 126-156;296-325, ASN_GLYCOSYLATION 40-43; 1.193; CK2_PHOSPHO_SITE 42-45;247-265, PKC_PHOSPHO_SITE 321-323; 1.134; MYRISTYL 243-248; 472-477,CK2_PHOSPHO_SITE 152-155; 1.034; PKC_PHOSPHO_SITE 42-44; 482-528,CK2_PHOSPHO_SITE 82-85; 1.182; MYRISTYL 163-168; MYRISTYL 596-602,619-624; MYRISTYL 129-134; 1.04; PKC_PHOSPHO_SITE 117-119; 224-241,CK2_PHOSPHO_SITE 189-192; 1.144; PKC_PHOSPHO_SITE 69-71; 123-151, 1.17;575-589, 1.06; 538-543, 1.067; 9-36, 1.166; 560-572, 1.094; 94-110,1.205; DEX0455_031.aa.2 Y 0 - 112-118, PKC_PHOSPHO_SITE 161-163; TNFR_c643-80; o1-166; 1.092; MYRISTYL 65-70; TNFR 43-80; 123-151,PKC_PHOSPHO_SITE 117-119; TNFR_NGFR_2_1 1.17; CK2_PHOSPHO_SITE 87-90;42-80; 51-86, MYRISTYL 129-134; TNFR_NGFR_2_2 1.191; CK2_PHOSPHO_SITE42-45; 82-124; TNFR 94-110, CK2_PHOSPHO_SITE 82-85; 83-124; TNFR 1.205;PKC_PHOSPHO_SITE 42-44; 126-160; 9-36, ASN_GLYCOSYLATION 40-43;TNFR_NGFR_1 43-80; 1.166; PKC_PHOSPHO_SITE 69-71; TNFR_NGFR_1CK2_PHOSPHO_SITE 140-143; 83-126; TNFR_c6 PKC_PHOSPHO_SITE 118-120;126-156; MYRISTYL 23-28; TNFR_c6 83-124; CAMP_PHOSPHO_SITE 119-122;CYS_RICH 58-148; TYR_PHOSPHO_SITE 44-51; CK2_PHOSPHO_SITE 152-155;DEX0455_031.or.f.2 N 1 - 266-272, PKC_PHOSPHO_SITE 293-295; TNFR_NGFR_239-80; o1-95; 1.04; PKC_PHOSPHO_SITE 5-7; PRO_RICH tm96-118; 81-87,MYRISTYL 72-77; MYRISTYL 237-272; TNFR i119-305; 1.087; 65-70;PKC_PHOSPHO_SITE 40-80; 11-29, 52-54; MYRISTYL 33-38; 1.128; MYRISTYL217-222; 284-291, PKC_PHOSPHO_SITE 79-81; 1.063; ASN_GLYCOSYLATION47-50; 97-134, MYRISTYL 289-294; 1.216; CK2_PHOSPHO_SITE 59-62; 208-213,CK2_PHOSPHO_SITE 193-196; 1.067; MYRISTYL 222-227; MYRISTYL 35-43, 1-6;1.196; 152-198, 1.182; 245-259, 1.06; 63-70, 1.08; 52-59, 1.113;230-242, 1.094; 142-147, 1.034; DEX0455_031.aa.3 Y 0 - 13-25, MYRISTYL178-183; MYRISTYL PRO_RICH 126-161; o1-194; 1.182; 106-111; MYRISTYL111-116; 31-36, PKC_PHOSPHO_SITE 182-184; 1.034; CAMP_PHOSPHO_SITE 9-12;41-87, CK2_PHOSPHO_SITE 82-85; 1.182; 155-161, 1.04; 119-131, 1.094;97-102, 1.067; 134-148, 1.06; 173-180, 1.063; DEX0455_032.aa.1 N 0 -42-50, PKC_PHOSPHO_SITE 152-154; o1-241; 1.149; PKC_PHOSPHO_SITE168-170; 84-96, 1.1; ASN_GLYCOSYLATION 39-42; 216-238, CK2_PHOSPHO_SITE206-209; 1.152; CK2_PHOSPHO_SITE 204-207; 172-179, PKC_PHOSPHO_SITE112-114; 1.085; ASN_GLYCOSYLATION 142-145; 22-32, CK2_PHOSPHO_SITE59-62; 1.209; CK2_PHOSPHO_SITE 193-196; 130-141, MYRISTYL 37-42; 1.11;CK2_PHOSPHO_SITE 169-172; 144-168, CK2_PHOSPHO_SITE 112-115; 1.133;ASN_GLYCOSYLATION 104-107; 198-204, CAMP_PHOSPHO_SITE 33-36; 1.108;CK2_PHOSPHO_SITE 92-95; 69-78, 1.125; DEX0455_033.aa.1 Y 5 - 34-40,PKC_PHOSPHO_SITE 248-250; VACATPASE 149-175; i1-6; 1.091; MYRISTYL53-58; MYRISTYL ATP-synt_C tm7-29; 4-32, 161-166; MYRISTYL 104-109;49-114; o30-48; 1.218; MYRISTYL 139-144; MYRISTYL VACATPASE 176-199;89-113, 183-188; MYRISTYL 159-164; VACATPASE tm49-71; 1.207;PKC_PHOSPHO_SITE 233-235; 65-89; ATP- i72-90; 234-258, MYRISTYL 141-146;MYRISTYL synt_C 135-200; tm91-113; 1.182; 64-69; MYRISTYL 156-161;o114-141; 203-232, CK2_PHOSPHO_SITE 27-30; tm142-164; 1.183; MYRISTYL10-15; MYRISTYL i165-175; 141-167, 190-195; MYRISTYL 23-28; tm176-198;1.258; CK2_PHOSPHO_SITE 119-122; o199-261; 169-201, MYRISTYL 68-73;MYRISTYL 1.2; 55-60; MYRISTYL 152-157; 53-74, 1.179; 78-84, 1.057;DEX0455_034.aa.1 Y 1 - 315-320, MYRISTYL 281-286; MYRISTYL ldl_recept_ai1-11; 1.032; 457-462; PKC_PHOSPHO_SITE 333-371; tm12-34; 247-254,450-452; ASN_GLYCOSYLATION Kunitz_BPTI o35-499; 1.118; 235-238;ASN_GLYCOSYLATION 250-300; 434-444, 66-69; MYRISTYL 423-428;sp_Q99J04_Q99J04_MOUSE 1.138; MYRISTYL 454-459; MYRISTYL 250-300;409-419, 282-287; PKC_PHOSPHO_SITE Kunitz_BPTI 1.088; 80-82; MYRISTYL310-315; 391-441; LDLa 328-355, CK2_PHOSPHO_SITE 225-228; 334-371;1.171; MYRISTYL 426-431; MYRISTYL LDLRA_2 334-370; 270-283, 422-427;MYRISTYL 161-166; LDLRA_1 1.163; CK2_PHOSPHO_SITE 374-377; 347-369;379-385, RGD 193-195; MYRISTYL 472-477; BPTI_KUNITZ_2_2 1.079; MYRISTYL212-217; 391-441; 113-132, MYRISTYL 29-34; MYRISTYL BPTI_KUNITZ_1 1.192;313-318; MYRISTYL 482-487; 419-437; 142-152, MYRISTYL 43-48;BPTI_KUNITZ_1 1.084; PKC_PHOSPHO_SITE 242-244; 278-296; 366-372,PKC_PHOSPHO_SITE 440-442; BPTI_KUNITZ_2_1 1.056; PKC_PHOSPHO_SITE490-492; 250-300; 10-33, PKC_PHOSPHO_SITE 148-150; BASICPTASE 275-285;1.215; CK2_PHOSPHO_SITE 350-353; KU 389-442; 36-53, MYRISTYL 494-499;sp_Q99J04_Q99J04_MOUSE 1.085; PKC_PHOSPHO_SITE 253-255; 391-441; 84-105,CK2_PHOSPHO_SITE 74-77; BASICPTASE 1.209; MYRISTYL 285-290; 426-441;55-67, PKC_PHOSPHO_SITE 386-388; BASICPTASE 247-261; 1.131; KU 248-301;168-183, 1.161; 388-403, 1.136; 235-243, 1.176; 256-262, 1.043; 216-227,1.151; 293-303, 1.148; 462-486, 1.137; DEX0455_034.aa.3 Y 1 - 315-320,ASN_GLYCOSYLATION 235-238; BPTI_KUNITZ_2 i1-11; 1.032; MYRISTYL 285-290;250-300; tm12-34; 270-283, CK2_PHOSPHO_SITE 74-77; BASICPTASE 247-261;o35-344; 1.163; PKC_PHOSPHO_SITE 242-244; sp_Q99J04_Q99J04_MOUSE293-303, MYRISTYL 282-287; 250-300; 1.148; CK2_PHOSPHO_SITE 225-228; KU248-301; 142-152, MYRISTYL 281-286; BPTI_KUNITZ_1 1.084;PKC_PHOSPHO_SITE 253-255; 278-296; 10-33, MYRISTYL 43-48; RGD 193-195;BASICPTASE 275-285; 1.215; MYRISTYL 161-166; BASICPTASE 36-53,ASN_GLYCOSYLATION 66-69; 285-300; 1.085; PKC_PHOSPHO_SITE 148-150;Kunitz_BPTI 168-183, MYRISTYL 212-217; MYRISTYL 250-300; 1.161; 313-318;MYRISTYL 29-34; 216-227, PKC_PHOSPHO_SITE 80-82; 1.151; MYRISTYL310-315; 330-341, 1.103; 256-262, 1.043; 84-105, 1.209; 55-67, 1.131;113-132, 1.192; 247-254, 1.118; 235-243, 1.176; DEX0455_034.aa.4 N 0 -431-437, CK2_PHOSPHO_SITE 439-442; LDLRA_1 412-434; o1-479; 1.056;MYRISTYL 94-99; KU 313-366; 207-217, CK2_PHOSPHO_SITE 290-293; LDLa399-436; 1.084; PKC_PHOSPHO_SITE 451-453; BASICPTASE 335-348, MYRISTYL226-231; MYRISTYL 340-350; 1.163; 277-282; PKC_PHOSPHO_SITE BASICPTASE312-326; 444-450, 307-309; MYRISTYL 462-467; Kunitz_BPTI 1.079; MYRISTYL378-383; 315-365; 300-308, CK2_PHOSPHO_SITE 415-418;sp_Q99J04_Q99J04_MOUSE 1.176; MYRISTYL 350-355; 315-365; 9-16, 1.07;PKC_PHOSPHO_SITE 213-215; BASICPTASE 101-118, ASN_GLYCOSYLATION 131-134;350-365; 1.085; MYRISTYL 347-352; MYRISTYL ldl_recept_a 380-385,375-380; PKC_PHOSPHO_SITE 398-436; 1.032; 318-320; MYRISTYL 346-351;BPTI_KUNITZ_2 54-61, MYRISTYL 464-469; 315-365; 1.121; CK2_PHOSPHO_SITE139-142; LDLRA_2 399-435; 120-132, MYRISTYL 108-113; BPTI_KUNITZ_11.131; PKC_PHOSPHO_SITE 145-147; 343-361; 233-248, ASN_GLYCOSYLATION300-303; 1.161; RGD 258-260; AMIDATION 61-64; 312-319, 1.118; 75-98,1.215; 178-197, 1.192; 466-476, 1.107; 393-420, 1.171; 281-292, 1.151;321-327, 1.043; 149-170, 1.209; 457-463, 1.098; 358-368, 1.148; 37-46,1.091; DEX0455_035.aa.1 N 1 - 81-101, MYRISTYL 54-59; MYRISTYL i1-92;1.213; 40-45; PKC_PHOSPHO_SITE tm93-115; 103-118, 119-121; o116-121;1.241; 54-62, 1.049; DEX0455_035.orf.2 N 1 - 21-32, PKC_PHOSPHO_SITE30-32; o1-125; 1.239; MYRISTYL 46-51; MYRISTYL tm126-148; 111-146,45-50; MYRISTYL 7-12; i149-149; 1.245; MYRISTYL 49-54; 57-64,PKC_PHOSPHO_SITE 53-55; 1.082; 69-84, 1.089; 4-11, 1.052; 86-95, 1.131;34-47, 1.143; DEX0455_035.aa.2 N 1 - 54-62, MYRISTYL 54-59; i1-92;1.049; PKC_PHOSPHO_SITE 119-121; tm93-115; 103-118, MYRISTYL 40-45;o116-121; 1.241; 81-101, 1.213; DEX0455_035.orf.3 N 1 - 34-47, MYRISTYL7-12; o1-125; 1.143; PKC_PHOSPHO_SITE 53-55; tm126-148; 57-64, MYRISTYL45-50; MYRISTYL i149-149; 1.082; 49-54; MYRISTYL 46-51; 21-32,PKC_PHOSPHO_SITE 30-32; 1.239; 86-95, 1.131; 4-11, 1.052; 111-146,1.245; 69-84, 1.089; DEX0455_035.aa.3 Y 1 - 34-42, MYRISTYL 20-25;MYRISTYL o1-71; 1.049; 34-39; PKC_PHOSPHO_SITE tm72-94; 61-81, 99-101;i95-101; 1.213; 83-98, 1.241; 4-12, 1.132; DEX0455_036.orf.1 N 1 -39-66, TYR_PHOSPHO_SITE 68-75; o1-40; 1.248; PKC_PHOSPHO_SITE 66-68;tm41-63; 76-92, MYRISTYL 61-66; i64-95; 1.111; CK2_PHOSPHO_SITE 87-90;15-24, PKC_PHOSPHO_SITE 65-67; 1.133; ASN_GLYCOSYLATION 11-14; MYRISTYL53-58; DEX0455_036.aa.1 N 1 - 53-80, TYR_PHOSPHO_SITE 82-89;G_PROTEIN_RECEP_F1_1 o1-54; 1.248; MYRISTYL 75-80; 18-34; tm55-77; 4-16,CK2_PHOSPHO_SITE 101-104; i78-109; 1.142; PKC_PHOSPHO_SITE 80-82; 29-38,MYRISTYL 67-72; 1.133; ASN_GLYCOSYLATION 25-28; 90-106, PKC_PHOSPHO_SITE79-81; 1.111; MYRISTYL 10-15; DEX0455_036.aa.2 N 0 - 427-433,PKC_PHOSPHO_SITE 1000-1002; SEA_1 757-823; o1-1485; 1.051; MYRISTYL191-196; SEA_2 913-979; 715-725, CK2_PHOSPHO_SITE 440-443; 1.093;ASN_GLYCOSYLATION 338-341; 1161-1180, TYR_PHOSPHO_SITE 237-245; 1.113;CK2_PHOSPHO_SITE 986-989; 1009-1017, ASN_GLYCOSYLATION 806-809; 1.062;PKC_PHOSPHO_SITE 1415-1417; 1369-1374, ASN_GLYCOSYLATION 1.054;1385-1388; MYRISTYL 35-40; 1428-1480, PKC_PHOSPHO_SITE 837-839; 1.146;ASN_GLYCOSYLATION 478-481; 673-683, PKC_PHOSPHO_SITE 1148-1150; 1.16;CK2_PHOSPHO_SITE 82-85; 594-600, MYRISTYL 124-129; 1.049;PKC_PHOSPHO_SITE 525-527; 170-199, ASN_GLYCOSYLATION 457-460; 1.136;MYRISTYL 436-441; 1388-1401, PKC_PHOSPHO_SITE 318-320; 1.161;CK2_PHOSPHO_SITE 550-553; 126-132, CK2_PHOSPHO_SITE 1275-1278; 1.062;CK2_PHOSPHO_SITE 50-53; 809-823, CK2_PHOSPHO_SITE 362-365; 1.119;PKC_PHOSPHO_SITE 102-104; 405-413, CK2_PHOSPHO_SITE 674-677; 1.091;MYRISTYL 47-52; 104-110, ASN_GLYCOSYLATION 790-793; 1.07;ASN_GLYCOSYLATION 1235-1238; 480-511, ASN_GLYCOSYLATION 1.148;1365-1368; 1405-1417, PKC_PHOSPHO_SITE 681-683; 1.159; CK2_PHOSPHO_SITE862-865; 1356-1366, ASN_GLYCOSYLATION 1029-1032; 1.086; PKC_PHOSPHO_SITE895-901, 1038-1040; MYRISTYL 659-664; 1.051; ASN_GLYCOSYLATION 49-61,634-637; PKC_PHOSPHO_SITE 1.148; 636-638; ASN_GLYCOSYLATION 73-89,1081-1084; MYRISTYL 1126-1131; 1.07; MYRISTYL 954-959; 114-121,CK2_PHOSPHO_SITE 206-209; 1.085; PKC_PHOSPHO_SITE 1103-1105; 14-43,ASN_GLYCOSYLATION 1.136; 650-653; CK2_PHOSPHO_SITE 416-422, 518-521;PKC_PHOSPHO_SITE 1.032; 258-260; PKC_PHOSPHO_SITE 1195-1210, 1097-1099;1.091; ASN_GLYCOSYLATION 1117-1120; 873-880, MYRISTYL 983-988; 1.078;ASN_GLYCOSYLATION 1101-1104; 341-355, ASN_GLYCOSYLATION 1.139; 769-772;ASN_GLYCOSYLATION 1061-1081, 301-304; MYRISTYL 503-508; 1.165;ASN_GLYCOSYLATION 1018-1021; 1051-1059, ASN_GLYCOSYLATION 1.101;322-325; ASN_GLYCOSYLATION 135-145, 925-928; PKC_PHOSPHO_SITE 1.171;746-748; ASN_GLYCOSYLATION 572-578, 613-616; PKC_PHOSPHO_SITE 1.043;948-950; PKC_PHOSPHO_SITE 537-557, 786-788; CK2_PHOSPHO_SITE 1.079;830-833; PKC_PHOSPHO_SITE 603-620, 162-164; MYRISTYL 1255-1260; 1.171;PKC_PHOSPHO_SITE 1341-1351, 347-349; PKC_PHOSPHO_SITE 1.091; 882-884;PKC_PHOSPHO_SITE 742-747, 942-944; MYRISTYL 203-208; 1.017; MYRISTYL971-976; 1276-1305, PKC_PHOSPHO_SITE 324-326; 1.178; ASN_GLYCOSYLATION946-949; 1022-1027, PKC_PHOSPHO_SITE 792-794; 1.076; CK2_PHOSPHO_SITE1173-1176; 853-869, PKC_PHOSPHO_SITE 1.079; 570-572; PKC_PHOSPHO_SITE987-998, 733-735; PKC_PHOSPHO_SITE 1.127; 1268-1270; MYRISTYL 1227-1232;750-756, MYRISTYL 904-909; 1.049; PKC_PHOSPHO_SITE 213-215; 1241-1253,PKC_PHOSPHO_SITE 1337-1339; 1.146; PKC_PHOSPHO_SITE 260-266, 1231-1233;1.074; TYR_PHOSPHO_SITE 1002-1009; 561-568, PKC_PHOSPHO_SITE 1.078;168-170; MYRISTYL 815-820; 517-527, ASN_GLYCOSYLATION 166-169; 1.127;PKC_PHOSPHO_SITE 474-476; 583-589, CK2_PHOSPHO_SITE 1425-1428; 1.035;MYRISTYL 1426-1431; 1255-1269, CK2_PHOSPHO_SITE 1141-1144; 1.16;ASN_GLYCOSYLATION 437-443, 10-13; ASN_GLYCOSYLATION 1.069; 1214-1217;361-374, PKC_PHOSPHO_SITE 57-59; 1.127; PKC_PHOSPHO_SITE 630-632;649-667, PKC_PHOSPHO_SITE 12-14; 1.12; MYRISTYL 1422-1427; 1120-1134,PKC_PHOSPHO_SITE 1193-1195; 1.119; ASN_GLYCOSYLATION 759-769, 145-148;PKC_PHOSPHO_SITE 1.186; 6-8; 1142-1150, 1.127; 1311-1324, 1.069;448-457, 1.171; 205-221, 1.105; 1029-1037, 1.068; 529-535, 1.029;950-979, 1.128; 229-257, 1.102; 904-925, 1.198; 271-277, 1.063; 697-708,1.073; 326-335, 1.128; 1105-1114, 1.128; 794-806, 1.128; 93-101, 1.078;385-396, 1.062; 829-839, 1.135; 1040-1046, 1.055; 884-890, 1.07;1184-1192, 1.078; 638-647, 1.128; 282-301, 1.181; DEX0455_036.orf.3 N1 - MYRISTYL 12-17; o1-56; PKC_PHOSPHO_SITE 81-83; tm57-79;CK2_PHOSPHO_SITE 103-106; i80-111; TYR_PHOSPHO_SITE 84-91;ASN_GLYCOSYLATION 11-14; PKC_PHOSPHO_SITE 82-84; MYRISTYL 69-74;MYRISTYL 11-16; ASN_GLYCOSYLATION 10-13; TYR_PHOSPHO_SITE 6-12; MYRISTYL77-82; DEX0455_036.aa.3 N 1 - 8-16, 1.19; MYRISTYL 53-58; o1-32; 68-84,TYR_PHOSPHO_SITE 60-67; tm33-55; 1.111; CK2_PHOSPHO_SITE 79-82; i56-87;31-58, PKC_PHOSPHO_SITE 58-60; 1.248; MYRISTYL 45-50; PKC_PHOSPHO_SITE57-59; DEX0455_036.orf.4 N 0 - 20-29, AMIDATION 34-37; o1-92; 1.064;PKC_PHOSPHO_SITE 51-53; 41-53, MYRISTYL 56-61; 1.181; PKC_PHOSPHO_SITE88-90; 62-72, PKC_PHOSPHO_SITE 62-64; 1.212; MYRISTYL 61-66; 4-10,1.151; DEX0455_036.aa.4 N 1 - 64-80, PKC_PHOSPHO_SITE 54-56; o1-28;1.111; MYRISTYL 49-54; MYRISTYL tm29-51; 27-54, 41-46; CK2_PHOSPHO_SITEi52-83; 1.248; 75-78; PKC_PHOSPHO_SITE 4-13, 53-55; TYR_PHOSPHO_SITE1.104; 56-63; DEX0455_037.aa.1 Y 0 - 199-205, MYRISTYL 124-129;PGNDSYNTHASE o1-225; 1.08; CK2_PHOSPHO_SITE 154-157; 74-92; 60-72,PKC_PHOSPHO_SITE 189-191; PGNDSYNTHASE 1.178; PKC_PHOSPHO_SITE 106-108;31-54; 150-159, CK2_PHOSPHO_SITE 109-112; PGNDSYNTHASE 1.178; MYRISTYL129-134; 57-67; 161-169, ASN_GLYCOSYLATION 78-81; LIPOCALIN 33-46; 1.13;PKC_PHOSPHO_SITE 109-111; lipocalin 116-126, MYRISTYL 144-149; 38-221;1.06; CK2_PHOSPHO_SITE 158-161; 181-186, MYRISTYL 100-105; MYRISTYL1.025; 133-138; ASN_GLYCOSYLATION 45-52, 51-54; MYRISTYL 76-81; 1.052;MYRISTYL 148-153; 8-33, PKC_PHOSPHO_SITE 218-220; 1.189; MYRISTYL 47-52;210-219, 1.123; 137-143, 1.07; 94-108, 1.076; DEX0455_037.orf.2 N 0 -294-307, PKC_PHOSPHO_SITE 215-217; PRICHEXTENSN o1-349; 1.148;PKC_PHOSPHO_SITE 173-175; 247-263; 108-114, MYRISTYL 185-190;PRICHEXTENSN 1.075; AMIDATION 123-126; 172-184; 200-209,PKC_PHOSPHO_SITE 4-6; PRICHEXTENSN 1.156; MYRISTYL 190-195; 339-349;320-335, CAMP_PHOSPHO_SITE 228-231; PRICHEXTENSN 1.295; PKC_PHOSPHO_SITE179-181; 148-164; 263-275, MYRISTYL 223-228; MYRISTYL 1.199; 116-121;PKC_PHOSPHO_SITE 15-38, 83-85; PKC_PHOSPHO_SITE 1.169; 226-228;CK2_PHOSPHO_SITE 246-252, 256-259; PKC_PHOSPHO_SITE 1.033; 120-122;AMIDATION 226-229; 6-12, PKC_PHOSPHO_SITE 243-245; 1.064;PKC_PHOSPHO_SITE 105-107; 87-93, MYRISTYL 283-288; 1.037; MYRISTYL287-292; 237-242, PKC_PHOSPHO_SITE 95-97; 1.056; MYRISTYL 195-200;MYRISTYL 45-70, 193-198; MYRISTYL 288-293; 1.189; MYRISTYL 275-280;MYRISTYL 132-149, 285-290; CAMP_PHOSPHO_SITE 1.075; 1-4; MYRISTYL99-104; 97-102, 1.067; 338-346, 1.088; 159-172, 1.15; 309-315, 1.106;219-225, 1.098; DEX0455_037.aa.2 Y 0 - 369-374, PKC_PHOSPHO_SITE 83-85;LIPOCALIN 256-269; o1-413; 1.025; MYRISTYL 270-275; A1MCGLOBULIN283-295, PKC_PHOSPHO_SITE 329-331; 269-280; 1.178; MYRISTYL 62-67;MYRISTYL lipocalin 261-409; 349-357, 236-241; MYRISTYL 171-176;MAJORURINARY 1.13; PKC_PHOSPHO_SITE 406-408; 263-281; 338-347, AMIDATION256-259; VNEBNERGLAND 1.178; MYRISTYL 154-159; MYRISTYL 300-312; 50-56,168-173; AMIDATION 86-89; PGNDSYNTHASE 1.037; MYRISTYL 190-195; 368-382;268-275, CK2_PHOSPHO_SITE 342-345; VNEBNERGLAND 1.052; PKC_PHOSPHO_SITE216-218; 371-394; 387-393, MYRISTYL 336-341; MYRISTYL LIPOCALIN 343-355;1.08; 186-191; CK2_PHOSPHO_SITE LIPOCALIN 193-201, 346-349;ASN_GLYCOSYLATION 260-272; 1.082; 301-304; PKC_PHOSPHO_SITE VNEBNERGLAND317-332, 162-164; CK2_PHOSPHO_SITE 260-274; 1.076; 177-180; MYRISTYL256-261; PGNDSYNTHASE 218-224, MYRISTYL 323-328; 385-403; 1.049;ASN_GLYCOSYLATION 274-277; LIPOCALIN 371-386; 231-240, MYRISTYL 170-175;A1MCGLOBULIN 1.065; PKC_PHOSPHO_SITE 377-379; 366-387; 60-65,PKC_PHOSPHO_SITE 58-60; MAJORURINARY 1.067; MYRISTYL 299-304; 393-410;71-77, ASN_GLYCOSLATION 226-229; A1MCGLOBULIN 1.075; MYRISTYL 79-84;394-413; 129-135; PKC_PHOSPHO_SITE 46-48; PGNDSYNTHASE 1.033;PKC_PHOSPHO_SITE 68-70; 280-290; 8-33 MAJORURINARY 1.189; 365-386;141-148, PGNDSYNTHASE 1.121; 332-335; 95-113, A1MCGLOBULIN 1.107;334-353; 398-407, PGNDSYNTHASE 1.123; 254-277; PGNDSYNTHASE 297-315;DEX0455_037.aa.3 Y 0 - 95-112, MYRISTYL 304-309; MYRISTYL GLY_RICH236-395; o1-410; 1.075; 251-256; MYRISTYL 336-341; 209-215, MYRISTYL264-269; 1.033; AMIDATION 285-288; 163-172, MYRISTYL 148-153; 1.156;CAMP_PHOSPHO_SITE 191-194; 200-205, MYRISTYL 282-287; MYRISTYL 1.056;156-161; MYRISTYL 153-158; 60-65, AMIDATION 189-192; 1.067;PKC_PHOSPHO_SITE 189-191; 292-298, MYRISTYL 250-255; 1.068;PKC_PHOSPHO_SITE 136-138; 370-376, PKC_PHOSPHO_SITE 142-144; 1.106;MYRISTYL 299-304; 381-396, AMIDATION 86-89; MYRISTYL 1.295; 238-243;PKC_PHOSPHO_SITE 50-56, 178-180; PKC_PHOSPHO_SITE 1.037; 58-60; MYRISTYL330-335; 226-238, AMIDATION 339-342; 1.199; MYRISTYL 79-84; 281-288,PKC_PHOSPHO_SITE 68-70; 1.078; MYRISTYL 186-191; MYRISTYL 122-135,318-323; PKC_PHOSPHO_SITE 1.15; 206-208; CK2_PHOSPHO_SITE 71-77,219-222; MYRISTYL 322-327; 1.075; MYRISTYL 274-279; 345-351,PKC_PHOSPHO_SITE 83-85; 1.103; MYRISTYL 248-253; MYRISTYL 8-33, 246-251;PKC_PHOSPHO_SITE 1.189; 46-48; MYRISTYL 158-163; 182-188, MYRISTYL326-331; MYRISTYL 1.098; 62-67; 308-317, 1.074; 399-407, 1.088; 360-368,1.106; DEX0455_037.aa.4 Y 0 - 38-44, MYRISTYL 71-76; PGNDSYNTHASEo1-135; 1.052; PKC_PHOSPHO_SITE 99-101; 90-104; 8-36, MYRISTYL 54-59;PGNDSYNTHASE 1.181; ASN_GLYCOSYLATION 93-96; 107-125; 109-115, MYRISTYL21-26; 1.08; PKC_PHOSPHO_SITE 128-130; 46-89, 1.223; 120-129, 1.123;DEX0455_037.aa.5 N 0 - 110-116, MYRISTYL 62-67; MYRISTYL o1-150; 1.09;51-56; ASN_GLYCOSYLATION 11-27, 71-74; PKC_PHOSPHO_SITE 1.137; 33-35;MYRISTYL 74-79; 75-102, MYRISTYL 138-143; MYRISTYL 1.154; 65-70;MYRISTYL 69-74; 137-147, PKC_PHOSPHO_SITE 116-118; 1.065; MYRISTYL115-120; MYRISTYL 47-53, 105-110; CK2_PHOSPHO_SITE 1.067; 46-49; 38-45,1.081; DEX0455_037.aa.6 Y 0 - 149-158, MYRISTYL 100-105; MYRISTYLLIPOCALIN 33-46; o1-224; 1.178; 147-152; PKC_PHOSPHO_SITE lipocalin137-143, 188-190; MYRISTYL 47-52; 38-220; 1.07; ASN_GLYCOSYLATION 51-54;PGNDSYNTHASE 209-218, MYRISTYL 124-129; 31-54; 1.123; PKC_PHOSPHO_SITE106-108; PGNDSYNTHASE 116-126, CK2_PHOSPHO_SITE 109-112; 57-67; 1.06;MYRISTYL 129-134; PGNDSYNTHASE 198-204, CK2_PHOSPHO_SITE 153-156; 74-92;1.08; ASN_GLYCOSYLATION 78-81; 45-52, MYRISTYL 133-138; 1.052;PKC_PHOSPHO_SITE 109-111; 94-108, CK2_PHOSPHO_SITE 157-160; 1.076;MYRISTYL 76-81; 160-168, PKC_PHOSPHO_SITE 217-219; 1.13; 8-33, 1.189;60-72, 1.178; 180-185, 1.025; DEX0455_037.aa.7 Y 0 - 458-464, MYRISTYL156-161; MYRISTYL LIPOCALIN 354-367; o1-481; 1.07; 336-341;PKC_PHOSPHO_SITE PGNDSYNTHASE 281-288, 58-60; PKC_PHOSPHO_SITE 395-413;1.078; 68-70; MYRISTYL 79-84; PGNDSYNTHASE 381-393, CK2_PHOSPHO_SITE430-433; 352-375; 1.178; MYRISTYL 282-287; MYRISTYL GLY_RICH 236-355;122-135, 264-269; AMIDATION 285-288; PGNDSYNTHASE 1.15; MYRISTYL445-450; 378-388; 358-364, MYRISTYL 330-335; MYRISTYL 1.026; 318-323;PKC_PHOSPHO_SITE 308-317, 46-48; PKC_PHOSPHO_SITE 1.074; 136-138;PKC_PHOSPHO_SITE 226-238, 83-85; ASN_GLYCOSYLATION 1.199; 399-402;MYRISTYL 186-191; 71-77, MYRISTYL 450-455; MYRISTYL 1.075; 299-304;MYRISTYL 421-426; 200-205, CAMP_PHOSPHO_SITE 191-194; 1.056; MYRISTYL454-459; MYRISTYL 345-351, 238-243; PKC_PHOSPHO_SITE 1.103; 427-429;MYRISTYL 62-67; 209-215, PKC_PHOSPHO_SITE 206-208; 1.033; MYRISTYL246-251; 163-172, AMIDATION 86-89; MYRISTYL 1.156; 274-279;PKC_PHOSPHO_SITE 182-188, 189-191; MYRISTYL 397-402; 1.098; MYRISTYL368-373; MYRISTYL 292-298, 468-473; MYRISTYL 158-163; 1.068;PKC_PHOSPHO_SITE 142-144; 60-65, MYRISTYL 148-153; 1.067;ASN_GLYCOSYLATION 372-375; 415-429, CK2_PHOSPHO_SITE 219-222; 1.076;MYRISTYL 304-309; MYRISTYL 50-56, 250-255; MYRISTYL 251-256; 1.037;PKC_PHOSPHO_SITE 472-474; 95-112, MYRISTYL 322-327; MYRISTYL 1.075;153-158; AMIDATION 339-342; 366-373, MYRISTYL 326-331; 1.052; MYRISTYL248-253; 8-33, PKC_PHOSPHO_SITE 178-180; 1.189; PKC_PHOSPHO_SITE430-432; 437-447, AMIDATION 189-192; 1.06; DEX0455_038.aa.1 N 1 -605-611, AMIDATION 268-271; TROPOMYOSIN i1-8; 1.066; CK2_PHOSPHO_SITE423-426; 622-639; tm9-31; 944-955, AMIDATION 278-281; TROPOMYOSINo32-1088; 1.104; AMIDATION 288-291; 695-715; 810-816, PKC_PHOSPHO_SITE750-752; Rib_recp_KP_reg 1.069; CAMP_PHOSPHO_SITE 476-479; 33-716;542-551, PKC_PHOSPHO_SITE 722-724; LYS_RICH 47-82; 1.102;CK2_PHOSPHO_SITE 632-635; TROPOMYOSIN 674-692, PKC_PHOSPHO_SITE 164-166;764-787; 1.106; AMIDATION 248-251; TROPOMYOSIN 879-897, PKC_PHOSPHO_SITE209-211; 831-856; 1.086; AMIDATION 338-341; 765-778, PKC_PHOSPHO_SITE525-527; 1.082; PKC_PHOSPHO_SITE 481-483; 1006-1012, CK2_PHOSPHO_SITE781-784; 1.077; PKC_PHOSPHO_SITE 32-34; 518-531, CK2_PHOSPHO_SITE135-138; 1.078; ASN_GLYCOSYLATION 931-934; 856-863, CK2_PHOSPHO_SITE998-1001; 1.092; AMIDATION 228-231; 462-468, AMIDATION 318-321; 1.065;CK2_PHOSPHO_SITE 1059-1062; 174-186, AMIDATION 238-241; 1.219;CK2_PHOSPHO_SITE 37-40; 1080-1085, CK2_PHOSPHO_SITE 847-850; 1.064;CK2_PHOSPHO_SITE 408-411; 822-829, PKC_PHOSPHO_SITE 135-137; 1.06;AMIDATION 308-311; 144-172, AMIDATION 436-439; 1.186; AMIDATION 396-399;565-571, PKC_PHOSPHO_SITE 539-541; 1.09; AMIDATION 416-419; 841-849,CK2_PHOSPHO_SITE 615-618; 1.057; CK2_PHOSPHO_SITE 722-725; 712-722,AMIDATION 426-429; 1.142; PKC_PHOSPHO_SITE 615-617; 731-752, MYRISTYL186-191; 1.127; AMIDATION 446-449; 130-135, PKC_PHOSPHO_SITE 804-806;1.037; PKC_PHOSPHO_SITE 72-74; 661-667, AMIDATION 368-371; 1.036;CK2_PHOSPHO_SITE 775-778; 89-127, CK2_PHOSPHO_SITE 561-564; 1.18;CK2_PHOSPHO_SITE 828-831; 1039-1050, AMIDATION 218-221; 1.161; AMIDATION376-379; 904-911; PKC_PHOSPHO_SITE 902-904; 1.142; MYRISTYL 189-194;957-964, CK2_PHOSPHO_SITE 32-35; 1.055; CK2_PHOSPHO_SITE 664-667;1017-1027, ASN_GLYCOSYLATION 207-210; 1.15; CK2_PHOSPHO_SITE 36-39;973-986, AMIDATION 386-389; 1.075; AMIDATION 198-201; 915-930, AMIDATION328-331; 1.17; MYRISTYL 195-200; 780-793, PKC_PHOSPHO_SITE 1070-1072;1.075; AMIDATION 348-351; 493-510, AMIDATION 258-261; 1.135;ASN_GLYCOSYLATION 91-94; 8-31, PKC_PHOSPHO_SITE 1027-1029; 1.182;MYRISTYL 1031-1036; 594-602, 1.136; 616-631, 1.118; DEX0455_038.orf.3 N1 - 49-58, PKC_PHOSPHO_SITE 263-265; LYS_RICH 146-181; i1-107; 1.131;AMIDATION 357-360; Rib_recp_KP_reg tm108-130; 243-271, PKC_PHOSPHO_SITE234-236; 132-275; o131-440; 1.186; AMIDATION 297-300; 188-226, AMIDATION377-380; 1.18; AMIDATION 327-330; 107-130, CK2_PHOSPHO_SITE 136-139;1.182; CK2_PHOSPHO_SITE 234-237; 16-27, PKC_PHOSPHO_SITE 308-310; 1.089;AMIDATION 427-430; 64-96, CK2_PHOSPHO_SITE 135-138; 1.129; AMIDATION317-320; 229-234, AMIDATION 39-42; MYRISTYL 1.037; 70-75; AMIDATION347-350; 273-285, AMIDATION 417-420; 1.219; MYRISTYL 285-290; MYRISTYL294-299; ASN_GLYCOSYLATION 190-193; MYRISTYL 7-12; CK2_PHOSPHO_SITE131-134; AMIDATION 43-46; PKC_PHOSPHO_SITE 131-133; AMIDATION 367-370;PKC_PHOSPHO_SITE 32-34; AMIDATION 387-390; PKC_PHOSPHO_SITE 59-61;PKC_PHOSPHO_SITE 171-173; ASN_GLYCOSYLATION 306-309; AMIDATION 407-410;AMIDATION 337-340; MYRISTYL 288-293; DEX0455_038.aa.3 Y 1 - 174-186,ASN_GLYCOSYLATION 91-94; Rib_recp_KP_reg i1-8; 1.219; MYRISTYL 417-422;MYRISTYL 278-426; tm9-31; 415-423, 189-194; PKC_PHOSPHO_SITE LYS_RICH47-82; o32-521; 1.129; 438-440; PKC_PHOSPHO_SITE Rib_recp_KP_reg130-135, 452-454; MYRISTYL 186-191; 33-176; 1.037; PKC_PHOSPHO_SITE135-137; 396-413, AMIDATION 228-231; 1.186; PKC_PHOSPHO_SITE 209-211;8-31, AMIDATION 238-241; 1.182; PKC_PHOSPHO_SITE 519-521; 144-172,AMIDATION 198-201; 1.186; PKC_PHOSPHO_SITE 164-166; 339-377,CK2_PHOSPHO_SITE 32-35; 1.18; AMIDATION 248-251; 455-464,PKC_PHOSPHO_SITE 385-387; 1.102; AMIDATION 258-261; 507-515, MYRISTYL195-200; 1.136; CK2_PHOSPHO_SITE 135-138; 478-484, AMIDATION 278-281;1.09; PKC_PHOSPHO_SITE 72-74; 431-444, AMIDATION 308-311; 1.078;CK2_PHOSPHO_SITE 474-477; 380-385, CK2_PHOSPHO_SITE 413-416; 1.037;AMIDATION 218-221; 89-127, PKC_PHOSPHO_SITE 32-34; 1.18; AMIDATION318-321; CK2_PHOSPHO_SITE 385-388; AMIDATION 288-291; AMIDATION 268-271;CK2_PHOSPHO_SITE 37-40; AMIDATION 328-331; CK2_PHOSPHO_SITE 36-39;ASN_GLYCOSYLATION 207-210; DEX0455_039.aa.1 Y 0 - 53-71,PKC_PHOSPHO_SITE 72-74; LYS_RICH 141-161; o1-165; 1.107; MYRISTYL 41-46;MYRISTYL 74-80, 78-83; CK2_PHOSPHO_SITE 1.034; 110-113; AMIDATION157-160; 86-93, PKC_PHOSPHO_SITE 3-5; 1.108; CK2_PHOSPHO_SITE 121-124;6-30, MYRISTYL 76-81; 1.126; CK2_PHOSPHO_SITE 117-120; 34-40,CK2_PHOSPHO_SITE 119-122; 1.082; CK2_PHOSPHO_SITE 32-35; 125-132,AMIDATION 152-155; 1.062; CK2_PHOSPHO_SITE 66-69; MYRISTYL 45-50;DEX0455_039.aa.2 N 0 - 103-113, MYRISTYL 76-81; AMIDATION LYS_RICH238-258; o1-262; 1.095; 254-257; MYRISTYL 112-117; 74-80,PKC_PHOSPHO_SITE 3-5; 1.034; CK2_PHOSPHO_SITE 66-69; 210-229, AMIDATION249-252; 1.107; MYRISTYL 41-46; MYRISTYL 6-30, 173-178; MYRISTYL 45-50;1.126; PKC_PHOSPHO_SITE 72-74; 118-132, CK2_PHOSPHO_SITE 32-35; 1.11;MYRISTYL 78-83; 86-93, 1.108; 53-71, 1.107; 139-168, 1.129; 174-207,1.173; 34-40, 1.082; DEX0455_040.orf.1 Y 0 - CK2_PHOSPHO_SITE 51-54;BPTI_KUNITZ_2_1 o1-231; MYRISTYL 88-93; 56-106; CK2_PHOSPHO_SITE 98-101;BASICPTASE 53-67; RGD 219-221; BPTI_KUNITZ_1 PKC_PHOSPHO_SITE 223-225;179-197; KU 54-107; CK2_PHOSPHO_SITE 108-111; BASICPTASE MYRISTYL 91-96;91-106; PKC_PHOSPHO_SITE 190-192; sp_O43291_SPT2_HUMAN MYRISTYL 183-188;MYRISTYL 56-106; 212-217; MYRISTYL 42-47; sp_O43291_SPT2_HUMAN MYRISTYL204-209; 151-201; ASN_GLYCOSYLATION 112-115; Kunitz_BPTI MYRISTYL186-191; MYRISTYL 151-201; KU 216-221; ASN_GLYCOSYLATION 149-202; 75-78;MYRISTYL 24-29; Kunitz_BPTI 56-106; MYRISTYL 182-187; BASICPTASEPKC_PHOSPHO_SITE 119-121; 81-91; MYRISTYL 87-92; BPTI_KUNITZ_2_2151-201; BPTI_KUNITZ_1 84-102; DEX0455_040.aa.1 Y 0 - 60-70, MYRISTYL69-74, KU 131-184; o1-213; 1.189; CK2_PHOSPHO_SITE 80-83; Kunitz_BPTI38-88; 107-113, MYRISTYL 195-200; MYRISTYL BASICPTASE 1.087; 207-212;PKC_PHOSPHO_SITE 35-49; 147-153, 204-206; CK2_PHOSPHO_SITEsp_O43291_SPT2_HUMAN 1.047; 90-93; MYRISTYL 70-75; 133-183; 178-188,MYRISTYL 73-78; MYRISTYL BPTI_KUNITZ_1 1.133; 203-208; MYRISTYL 168-173;66-84; 81-91, ASN_GLYCOSYLATION 94-97; BPTI_KUNITZ_2_2 1.13;ASN_GLYCOSYLATION 57-60; 133-183; 130-136, PKC_PHOSPHO_SITE 172-174;BPTI_KUNITZ_1 1.11; MYRISTYL 6-11; MYRISTYL 161-179; 10-28, 165-170;PKC_PHOSPHO_SITE BASICPTASE 73-88; 1.181; 101-103; MYRISTYL 198-203;Kunitz_BPTI 138-145, MYRISTYL 164-169; 133-183; 1.083; CK2_PHOSPHO_SITE33-36; BPTI_KUNITZ_2_1 35-47, MYRISTYL 24-29; 38-88; KU 36-89; 1.25;sp_O43291_SPT2_HUMAN 38-88; BASICPTASE 63-73; DEX0455_040.aa.2 Y 0 -35-47, MYRISTYL 73-78; MYRISTYL Kunitz_BPTI 38-88; o1-242; 1.25; 6-11;MYRISTYL 168-173; KU 131-184; 107-113, ASN_GLYCOSYLATION 94-97;BPTI_KUNITZ_2_2 1.087; CK2_PHOSPHO_SITE 33-36; 133-183; 201-239,PKC_PHOSPHO_SITE 172-174; sp_O43291_SPT2_HUMAN 1.186; MYRISTYL 70-75;MYRISTYL 38-88; 178-186, 69-74; PKC_PHOSPHO_SITE BPTI_KUNITZ_1 1.133;101-103; ASN_GLYCOSYLATION 66-84; 130-136, 57-60; CK2_PHOSPHO_SITEsp_O43291_SPT2_HUMAN 1.11; 214-217; CK2_PHOSPHO_SITE 133-183; 138-145,90-93; MYRISTYL 164-169; BPTI_KUNITZ_2_1 1.083; MYRISTYL 24-29; 38-88;189-195, CK2_PHOSPHO_SITE 80-83; BPTI_KUNITZ_1 1.083; MYRISTYL 165-170;161-179; 10-28, Kunitz_BPTI 1.181; 133-183; 81-91, BASICPTASE 73-88;1.13; BASICPTASE 60-70, 63-73; KU 36-89; 1.189; BASICPTASE 147-153,35-49; 1.047; DEX0455_041.orf.1 N 0 - 16-21, PKC_PHOSPHO_SITE 21-23;o1-53; 1.006; PKC_PHOSPHO_SITE 42-44; 4-11, PKC_PHOSPHO_SITE 20-22;1.105; MYRISTYL 7-12; DEX0455_041.aa.1 N 0 - 33-38, MYRISTYL 28-33;MYRISTYL o1-43; 1.046; 6-11; ASN_GLYCOSYLATION 5-20, 32-35; 1.129,DEX0455_041.orf.2 N 0 - 4-17, ASN_GLYCOSYLATION 29-32; o1-66; 1.129;MYRISTYL 25-30; 30-35, PKC_PHOSPHO_SITE 55-57; 1.046; DEX0455_041.aa.2 Y0 - 6-18, i1-34; 1.141; 25-31, 1.103; DEX0455_042.orf.1 N 0 -PKC_PHOSPHO_SITE 3-5; o1-116; MYRISTYL 10-15; CK2_PHOSPHO_SITE 7-10;ASN_GLYCOSYLATION 75-78; AMIDATION 40-43; PKC_PHOSPHO_SITE 41-43;CK2_PHOSPHO_SITE 81-84; CK2_PHOSPHO_SITE 36-39; ASN_GLYCOSYLATION 34-37;CK2_PHOSPHO_SITE 72-75; TYR_PHOSPHO_SITE 51-59; CK2_PHOSPHO_SITE 93-96;ASN_GLYCOSYLATION 80-83; PKC_PHOSPHO_SITE 29-31; TYR_PHOSPHO_SITE 40-48;CK2_PHOSPHO_SITE 82-85; CK2_PHOSPHO_SITE 17-20; CK2_PHOSPHO_SITE 56-59;CAMP_PHOSPHO_SITE 69-72; CK2_PHOSPHO_SITE 71-74; CK2_PHOSPHO_SITE112-115; CK2_PHOSPHO_SITE 76-79; CAMP_PHOSPHO_SITE 42-45;TYR_PHOSPHO_SITE 50-57; PKC_PHOSPHO_SITE 44-46; CK2_PHOSPHO_SITE 77-80;TYR_PHOSPHO_SITE 24-31; CAMP_PHOSPHO_SITE 4-7; PKC_PHOSPHO_SITE 113-115;PKC_PHOSPHO_SITE 71-73; TYR_PHOSPHO_SITE 35-41; DEX0455_042.aa.1 N 0 -MYRISTYL 8-13; o1-122; CK2_PHOSPHO_SITE 87-90; PKC_PHOSPHO_SITE 9-11;CK2_PHOSPHO_SITE 99-102; PKC_PHOSPHO_SITE 47-49; AMIDATION 46-49;CK2_PHOSPHO_SITE 23-26; ASN_GLYCOSYLATION 40-43; TYR_PHOSPHO_SITE 30-37;CK2_PHOSPHO_SITE 88-91; MYRISTYL 16-21; PKC_PHOSPHO_SITE 35-37;CAMP_PHOSPHO_SITE 48-51; ASN_GLYCOSYLATION 7-10; PKC_PHOSPHO_SITE 87-89;TYR_PHOSPHO_SITE 41-47; CK2_PHOSPHO_SITE 42-45; DEX0455_043.orf.1 Y 0 -64-72, MYRISTYL 3-8; o1-86; 1.133; ASN_GLYCOSYLATION 60-63; 76-83,PKC_PHOSPHO_SITE 29-31; 1.14; MYRISTYL 64-69; MYRISTYL 27-38, 56-61;MYRISTYL 61-66; 1.086; 4-20, 1.192; 41-50, 1.137; DEX0455_043.aa.1 N 0 -11-26, CK2_PHOSPHO_SITE 24-27; o1-30; 1.155; DEX0455_043.orf.2 N 0 -CK2_PHOSPHO_SITE 94-97; o1-125; MYRISTYL 47-52; PKC_PHOSPHO_SITE 84-86;MYRISTYL 8-13; PKC_PHOSPHO_SITE 77-79; DEX0455_043.orf.3 N 0 - 89-95,PKC_PHOSPHO_SITE 42-44; i1-104; 1.052; CK2_PHOSPHO_SITE 34-37; 59-97,MYRISTYL 9-14; 1.023; PKC_PHOSPHO_SITE 45-47; 10-38, PKC_PHOSPHO_SITE3-5; 1.08; ASN_GLYCOSYLATION 11-14; DEX0455_044.aa.1 N 1 - 14-24,MYRISTYL 27-32; i1-31; 1.177; Tm32-54; 29-58, o55-61; 1.199;DEX0455_045.orf.1 N 0 - 178-190, AMIDATION 65-68; o1-193; 1.144;PKC_PHOSPHO_SITE 129-131; 135-145, MYRISTYL 10-15; 1.124;PKC_PHOSPHO_SITE 93-95; 121-128, MYRISTYL 81-86; 1.095;CAMP_PHOSPHO_SITE 175-178; 70-111, AMIDATION 173-176; 1.15;PKC_PHOSPHO_SITE 5-7; 25-46, CAMP_PHOSPHO_SITE 110-113; 1.115; MYRISTYL83-88; 51-66, CK2_PHOSPHO_SITE 167-170; 1.216; DEX0455_045.aa.1 N 0 -25-46, CK2_PHOSPHO_SITE 149-152; o1-163; 1.115; AMIDATION 65-68;121-128, PKC_PHOSPHO_SITE 5-7; 1.095; MYRISTYL 10-15; 51-66,CAMP_PHOSPHO_SITE 146-149; 1.216; MYRISTYL 81-86; 135-144,PKC_PHOSPHO_SITE 93-95; 1.081; CAMP_PHOSPHO_SITE 110-113; 70-111,MYRISTYL 83-88; 1.15; PKC_PHOSPHO_SITE 129-131; DEX0455_046.orf.1 N 0 -MYRISTYL 115-120; o1-227; PKC_PHOSPHO_SITE 3-5; MYRISTYL 97-102;MYRISTYL 133-138; CAMP_PHOSPHO_SITE 163-166; CK2_PHOSPHO_SITE 3-6;MYRISTYL 3-8; DEX0455_046.aa.1 N 0 - 4-11, MYRISTYL 90-95; MYRISTYLo1-198; 1.144; 71-76; CK2_PHOSPHO_SITE 51-59, 156-159; MYRISTYL 161-166;1.107; PKC_PHOSPHO_SITE 63-65; 160-184, MYRISTYL 153-158; MYRISTYL1.151; 149-154; PKC_PHOSPHO_SITE 15-25, 119-121; MYRISTYL 86-91; 1.11;MYRISTYL 157-162; MYRISTYL 93-99, 68-73; CAMP_PHOSPHO_SITE 1.11;120-123; MYRISTYL 104-109; 73-85, 1.118; 32-40, 1.076; 146-153, 1.088;DEX0455_047.orf.1 N 0 - 66-100, AMIDATION 14-17; o1-103; 1.232;PKC_PHOSPHO_SITE 73-75; 23-44, CK2_PHOSPHO_SITE 33-36; 1.101;PKC_PHOSPHO_SITE 59-61; 10-17, MYRISTYL 96-101; 1.088; DEX0455_047.aa.1Y 0 - 42-48, ASN_GLYCOSYLATION 32-35; o1-65; 1.073; CK2_PHOSPHO_SITE23-26; 55-62, ASN_GLYCOSYLATION 39-42; 1.119; MYRISTYL 19-24; 4-30,1.142; 32-40, 1.122; DEX0455_047.orf.2 N 0 - 10-17, AMIDATION 14-17;o1-103; 1.088; CK2_PHOSPHO_SITE 33-36; 66-100, MYRISTYL 96-101; 1.232;PKC_PHOSPHO_SITE 73-75; 23-44, PKC_PHOSPHO_SITE 59-61; 1.101;DEX0455_047.aa.2 N 0 - o1-27; DEX0455_048.aa.1 Y 0 - 111-117,TYR_PHOSPHO_SITE 105-112; o1-154; 1.077; MYRISTYL 80-85; 83-97,PKC_PHOSPHO_SITE 56-58; 1.104; CK2_PHOSPHO_SITE 37-40; 4-60,TYR_PHOSPHO_SITE 79-86; 1.197; 99-107, 1.051; 63-78, 1.095; 126-151,1.156; DEX0455_048.orf.2 N 0 - 151-173, PKC_PHOSPHO_SITE 169-171;o1-176; 1.203; MYRISTYL 83-88; 86-100, PKC_PHOSPHO_SITE 59-61; 1.104;TYR_PHOSPHO_SITE 108-115; 114-120, CK2_PHOSPHO_SITE 40-43; 1.077;TYR_PHOSPHO_SITE 82-89; 129-141, CK2_PHOSPHO_SITE 24-27; 1.156; 102-110,1.051; 66-81, 1.095; 4-63, 1.197; DEX0455_048.aa.2 N 0 - 39-50,TYR_PHOSPHO_SITE 203-210; o1-271; 1.182; PKC_PHOSPHO_SITE 154-156; 4-21,PKC_PHOSPHO_SITE 34-36; 1.232; RGD 26-28; 181-195, PKC_PHOSPHO_SITE264-266; 1.104; ASN_GLYCOSYLATION 95-98; 98-158, MYRISTYL 38-43; 1.148;PKC_PHOSPHO_SITE 21-23; 246-268, CK2_PHOSPHO_SITE 88-91; 1.203;TYR_PHOSPHO_SITE 177-184; 161-176, MYRISTYL 178-183; 1.095;CK2_PHOSPHO_SITE 135-138; 197-205, PKC_PHOSPHO_SITE 96-98; 1.051;CK2_PHOSPHO_SITE 119-122; 66-90, 1.192; 224-236, 1.156; 209-215, 1.077;57-62, 1.053; DEX0455_049.aa.1 N 1 - 199-209, PKC_PHOSPHO_SITE 243-245;THYROGLOBULIN_1 o1-219; 1.147; MYRISTYL 66-71; 49-77; tm220-242;129-139, TYR_PHOSPHO_SITE 105-111; thyroglobulin_1 i243-268; 1.104;MYRISTYL 77-82; 20-89; TY 50-93; 95-105, PKC_PHOSPHO_SITE 154-156;1.087; CK2_PHOSPHO_SITE 88-91; 4-24, MYRISTYL 217-222; MYRISTYL 1.212;9-14; PKC_PHOSPHO_SITE 81-83; 219-244, ASN_GLYCOSYLATION 152-155; 1.317;PKC_PHOSPHO_SITE 115-117; 58-63, ASN_GLYCOSYLATION 28-31; 1.099;AMIDATION 32-35; 145-153, MYRISTYL 29-34; 1.156; PKC_PHOSPHO_SITE125-127; 69-76, MYRISTYL 57-62; 1.121; CK2_PHOSPHO_SITE 81-84; 86-93,CK2_PHOSPHO_SITE 157-160; 1.085; PKC_PHOSPHO_SITE 90-92; 163-172,MYRISTYL 40-45; 1.122; ASN_GLYCOSYLATION 65-68; 176-182,PKC_PHOSPHO_SITE 182-184; 1.056; DEX0455_049.aa.2 N 1 - 237-246,MYRISTYL 10-15; TY 124-167; o1-293; 1.122; ASN_GLYCOSYLATION 139-142;thyroglobulin_1 tm294-316; 52-67, MYRISTYL 291-296; 94-163; i317-342;1.194; TYR_PHOSPHO_SITE 179-185; THYROGLOBULIN_1 169-179, MYRISTYL29-34; 123-151; 1.087; PKC_PHOSPHO_SITE 164-166; 132-137, MYRISTYL151-156; 1.099; PKC_PHOSPHO_SITE 228-230; 219-227, ASN_GLYCOSYLATION25-28; 1.156; CK2_PHOSPHO_SITE 231-234; 41-50, MYRISTYL 32-37; MYRISTYL1.059; 140-145; CK2_PHOSPHO_SITE 203-213, 155-158; PKC_PHOSPHO_SITE1.104; 317-319; MYRISTYL 103-108; 273-283, PKC_PHOSPHO_SITE 155-157;1.147; PKC_PHOSPHO_SITE 256-258; 250-256, MYRISTYL 114-119; 1.056;ASN_GLYCOSYLATION 226-229; 24-29, PKC_PHOSPHO_SITE 189-191; 1.038;MYRISTYL 131-136; 293-318, PKC_PHOSPHO_SITE 199-201; 1.317;CK2_PHOSPHO_SITE 162-165; 73-98, ASN_GLYCOSYLATION 102-105; 1.193;AMIDATION 106-109; 143-150, MYRISTYL 80-85; 1.121; 160-167, 1.085;DEX0455_049.aa.3 Y 0 - 45-70, MYRISTYL 112-117; thyroglobulin_1 o1-240;1.193; PKC_PHOSPHO_SITE 127-129; 66-135; TY 96-139; 4-22,PKC_PHOSPHO_SITE 136-138; THYROGLOBULIN_1 1.166; TYR_PHOSPHO_SITE151-157; 95-123; 132-139, MYRISTYL 10-15; AMIDATION 1.085; 78-81;ASN_GLYCOSYLATION 191-199, 198-201; MYRISTYL 86-91; 1.156;CK2_PHOSPHO_SITE 134-137; 24-39, MYRISTYL 75-80; 1.194; PKC_PHOSPHO_SITE171-173; 104-109, ASN_GLYCOSYLATION 74-77; 1.099; PKC_PHOSPHO_SITE200-202; 115-122, MYRISTYL 123-128; MYRISTYL 1.121; 52-57; MYRISTYL103-108; 175-185, CK2_PHOSPHO_SITE 127-130; 1.104; CK2_PHOSPHO_SITE203-206; 209-216, PKC_PHOSPHO_SITE 161-163; 1.122; ASN_GLYCOSYLATION111-114; 141-151, 1.087; 220-237, 1.155; DEX0455_049.aa.4 Y 1 - 191-198,PKC_PHOSPHO_SITE 212-214; thyroglobulin_1 o1-341; 1.121;CK2_PHOSPHO_SITE 203-206; 142-211; TY tm342-364; 251-261, AMIDATION154-157; 172-215; i365-390; 1.104; PKC_PHOSPHO_SITE 247-249;THYROGLOBULIN_1 4-23, PKC_PHOSPHO_SITE 365-367; 171-199; 1.166;PKC_PHOSPHO_SITE 94-96; 217-227, MYRISTYL 151-156; 1.087;PKC_PHOSPHO_SITE 304-306; 321-331, CK2_PHOSPHO_SITE 48-51; 1.147;MYRISTYL 10-15; MYRISTYL 298-304, 188-193; PKC_PHOSPHO_SITE 1.056;237-239; ASN_GLYCOSYLATION 341-366, 150-153; MYRISTYL 179-184; 1.317;TYR PHOSPHO_SITE 227-233; 208-215, PKC_PHOSPHO_SITE 70-72; 1.085; RGD66-68; 267-275, ASN_GLYCOSYLATION 274-277; 1.156; PKC_PHOSPHO_SITE203-205; 180-185, MYRISTYL 39-44; AMIDATION 1.099; 81-84; MYRISTYL128-133; 285-294, PKC_PHOSPHO_SITE 276-278; 1.122; MYRISTYL 162-167;92-115, ASN_GLYCOSYLATION 187-190; 1.194; MYRISTYL 199-204; 121-146,CK2_PHOSPHO_SITE 210-213; 1.193; MYRISTYL 339-344; 71-77,CK2_PHOSPHO_SITE 279-282; 1.09; DEX0455_049.aa.5 Y 1 - 4-22, MYRISTYL86-91; thyroglobulin_1 o1-265; 1.166; ASN_GLYCOSYLATION 198-201; 66-135;TY 96-139; tm266-288; 115-122, PKC_PHOSPHO_SITE 127-129; THYROGLOBULIN_1i289-314; 1.133; PKC_PHOSPHO_SITE 228-230; 95-123; 132-139, MYRISTYL75-80; MYRISTYL 1.085; 52-57; MYRISTYL 103-108; 222-228,CK2_PHOSPHO_SITE 127-130; 1.056; PKC_PHOSPHO_SITE 289-291; 191-199,PKC_PHOSPHO_SITE 200-202; 1.156; TYR_PHOSPHO_SITE 151-157; 245-255,MYRISTYL 123-128; 1.147; CK2_PHOSPHO_SITE 203-206; 141-151,PKC_PHOSPHO_SITE 136-138; 1.087; ASN_GLYCOSYLATION 111-114; 45-70,MYRISTYL 263-268; 1.193; AMIDATION 78-81; 209-218, CK2_PHOSPHO_SITE134-137; 1.122; ASN_GLYCOSYLATION 74-77; 175-185, PKC_PHOSPHO_SITE161-163; 1.104; PKC_PHOSPHO_SITE 171-173; 24-39, MYRISTYL 10-15;MYRISTYL 1.194; 112-117; 104-109, 1.099; 265-290, 1.317;DEX0455_050.orf.1 Y 1 - 60-71, CK2_PHOSPHO_SITE 72-75; PHE_RICH 18-29;i1-11; 1.212; PKC_PHOSPHO_SITE 39-41; tm12-31; 79-93, PKC_PHOSPHO_SITE113-115; o32-122; 1.103; ASN_GLYCOSYLATION 2-5; 97-119, CK2_PHOSPHO_SITE4-7; 1.218; 37-45, 1.137; 12-34, 1.192; DEX0455_050.aa.1 Y 0 - 9-25,PKC_PHOSPHO_SITE 4-6; ACTINS_2 29-37; o1-48; 1.107; CK2_PHOSPHO_SITE31-34; 40-45, MYRISTYL 16-21; 1.135; DEX0455_051.aa.1 N 0 - 130-149,TRY_PHOSPHO_SITE 182-189; PRO_RICH 407-449; o1-596; 1.131;PKC_PHOSPHO_SITE 463-465; SH3 351-410; 509-519, PKC_PHOSPHO_SITE167-169; SH3DOMAIN 1.077; MYRISTYL 459-464; MYRISTYL 368-383; SH3 40-45,530-535; CK2_PHOSPHO_SITE 354-409; 1.041; 46-49; CAMP_PHOSPHO_SITEsp_Q9GZQ2_Q9GZQ2_HUMAN 523-540, 65-68; CK2_PHOSPHO_SITE 360-403; 1.153;295-298; CK2_PHOSPHO_SITE SH3DOMAIN 215-230, 106-109; PKC_PHOSPHO_SITE354-364; 1.13; 241-243; MYRISTYL 524-529; SH3DOMAIN 396-408; 99-105,PKC_PHOSPHO_SITE 371-373; SH3 354-408; 1.045; MYRISTYL 506-511; 397-422,CK2_PHOSPHO_SITE 549-552; 1.135; CK2_PHOSPHO_SITE 12-15; 239-258,CK2_PHOSPHO_SITE 463-466; 1.127; CK2_PHOSPHO_SITE 13-16; 573-579,ASN_GLYCOSYLATION 2-5; 1.113; CK2_PHOSPHO_SITE 185-188; 327-334,MYRISTYL 26-31; 1.141; PKC_PHOSPHO_SITE 384-386; 369-383,CK2_PHOSPHO_SITE 574-577; 1.122; CK2_PHOSPHO_SITE 282-285; 428-443,PKC_PHOSPHO_SITE 260-262; 1.091; PKC_PHOSPHO_SITE 178-180; 470-477,CK2_PHOSPHO_SITE 74-77; 1.104; ASN_GLYCOSYLATION 231-234; 58-76,MYRISTYL 79-84; 1.133; PKC_PHOSPHO_SITE 68-70; 490-496, CK2_PHOSPHO_SITE260-263; 1.055; PKC_PHOSPHO_SITE 33-35; 554-568, ASN_GLYCOSYLATION366-369; 1.178; CK2_PHOSPHO_SITE 214-217; 500-506, MYRISTYL 103-108;1.046; CK2_PHOSPHO_SITE 565-568; 545-551, AMIDATION 163-166; 1.071;CK2_PHOSPHO_SITE 269-272; 120-128, 1.127; 354-361, 1.134; 174-182,1.075; 298-304, 1.052; 154-160, 1.084; 189-205, 1.127; 25-31, 1.047;DEX0455_051.aa.2 N 0 - 4-41, PKC_PHOSPHO_SITE 401-403; SH3DOMAIN274-286; o1-408; 1.232; CK2_PHOSPHO_SITE 341-344; SH3DOMAIN 67-83,CK2_PHOSPHO_SITE 63-66; 246-261; SH3 1.127; ASN_GLYCOSYLATION 109-112;232-286; 205-212, PKC_PHOSPHO_SITE 56-58; PRICHEXTENSN 1.141;PKC_PHOSPHO_SITE 138-140; 165-182; 306-321, PKC_PHOSPHO_SITE 249-251;PRICHEXTENSN 1.091; AMIDATION 401-404; 50-62; PRO_RICH 117-136,PKC_PHOSPHO_SITE 119-121; 285-327; 1.127; PKC_PHOSPHO_SITE 262-264;sp_Q9GZQ2_Q9GZQ2_HUMAN 232-239, CK2_PHOSPHO_SITE 138-141; 238-281;1.134; ASN_GLYCOSYLATION 244-247; SH3 229-288; 368-374, CK2_PHOSPHO_SITE147-150; SH3 232-287; 1.055; MYRISTYL 384-389; SH3DOMAIN 93-108,CK2_PHOSPHO_SITE 92-95; 232-242; 1.13; PKC_PHOSPHO_SITE 341-343;PRICHEXTENSN 275-300, MYRISTYL 337-342; 308-320; 1.135; TYR_PHOSPHO_SITE60-67; 176-182, CK2_PHOSPHO_SITE 160-163; 1.052; CK2_PHOSPHO_SITE173-176; 348-355, 1.104; 387-397, 1.077; 247-261, 1.122; 45-60, 1.079;378-384, 1.046; DEX0455_051.aa.3 N 0 - 383-393, CK2_PHOSPHO_SITE 88-91;sp_Q9GZQ2_Q9GZQ2_HUMAN o1-470; 1.077; CK2_PHOSPHO_SITE 423-426; 234-277;428-442, PKC_PHOSPHO_SITE 258-260; SH3 228-283; 1.178; CK2_PHOSPHO_SITE156-159; PRICHEXTENSN 344-351, CK2_PHOSPHO_SITE 169-172; 304-316; 1.104;CK2_PHOSPHO_SITE 59-62; SH3DOMAIN 228-238; 374-380, CK2_PHOSPHO_SITE143-146; PRO_RICH 1.046; MYRISTYL 380-385; 281-323; SH3 4-37,CK2_PHOSPHO_SITE 134-137; 225-284; 1.232; CK2_PHOSPHO_SITE 448-451;PRICHEXTENSN 41-56, ASN_GLYCOSYLATION 105-108; 46-58; 1.079;PKC_PHOSPHO_SITE 134-136; SH3DOMAIN 270-282; 271-296, PKC_PHOSPHO_SITE52-54; SH3DOMAIN 1.135; CK2_PHOSPHO_SITE 439-442; 242-257; SH3 447-453,CK2_PHOSPHO_SITE 337-340; 228-282; 1.113; PKC_PHOSPHO_SITE 115-117;PRICHEXTENSN 419-425, MYRISTYL 398-403; 161-178; 1.071; PKC_PHOSPHO_SITE337-339; 243-257, MYRISTYL 404-409; 1.122; TYR_PHOSPHO_SITE 56-63;113-132, ASN_GLYCOSYLATION 240-243; 1.127; PKC_PHOSPHO_SITE 245-247;228-235, MYRISTYL 333-338; 1.134; 302-317, 1.091; 172-178, 1.052;201-208, 1.141; 89-104, 1.13; 63-79, 1.127; 397-414, 1.153; 364-370,1.055; DEX0455_051.orf.4 N 0 - 378-384, PKC_PHOSPHO_SITE 341-343;PRO_RICH 285-327; o1-474; 1.046; PKC_PHOSPHO_SITE 262-264; SH3 229-288;45-60, CK2_PHOSPHO_SITE 173-176; PRICHEXTENSN 1.079; PKC_PHOSPHO_SITE119-121; 165-182; 306-321, CK2_PHOSPHO_SITE 63-66; SH3DOMAIN 274-286;1.091; CK2_PHOSPHO_SITE 138-141; SH3DOMAIN 176-182, CK2_PHOSPHO_SITE160-163; 246-261; 1.052; CK2_PHOSPHO_SITE 452-455; SH3DOMAIN 232-242;67-83, MYRISTYL 384-389; PRICHEXTENSN 1.127; PKC_PHOSPHO_SITE 138-140;308-320; 232-239, ASN_GLYCOSYLATION 109-112; PRICHEXTENSN 1.134;CK2_PHOSPHO_SITE 427-430; 50-62; 247-261, TYR_PHOSPHO_SITE 60-67;sp_Q9GZQ2_Q9GZQ2_HUMAN 1.122; PKC_PHOSPHO_SITE 249-251; 238-281; 93-108,CK2_PHOSPHO_SITE 341-344; SH3 232-287; 1.13; MYRISTYL 402-407; SH3232-286; 432-446, CK2_PHOSPHO_SITE 147-150; 1.178; MYRISTYL 408-413;117-136, CK2_PHOSPHO_SITE 443-446; 1.127; PKC_PHOSPHO_SITE 56-58;451-457, MYRISTYL 337-342; 1.113; CK2_PHOSPHO_SITE 92-95; 205-212,ASN_GLYCOSYLATION 244-247; 1.141; 4-41, 1.232; 348-355, 1.104; 275-300,1.135; 387-397, 1.077; 368-374, 1.055; 423-429, 1.071; 401-418, 1.153;DEX0455_051.orf.5 N 0 - 306-321, ASN_GLYCOSYLATION 244-247; PRO_RICH285-327; o1-474; 1.091; PKC_PHOSPHO_SITE 249-251; SH3 232-287; 93-108,CK2_PHOSPHO_SITE 341-344; PRICHEXTENSN 1.13; CK2_PHOSPHO_SITE 443-446;308-320; 232-239, MYRISTYL 402-407; SH3DOMAIN 246-261; 1.134;PKC_PHOSPHO_SITE 119-121; SH3DOMAIN 423-429, PKC_PHOSPHO_SITE 56-58;232-242; 1.071; CK2_PHOSPHO_SITE 160-163; PRICHEXTENSN 451-457,PKC_PHOSPHO_SITE 138-140; 165-182; SH3 1.113; CK2_PHOSPHO_SITE 63-66;232-286; 247-261, MYRISTYL 337-342; PRICHEXTENSN 1.122; TYR_PHOSPHO_SITE60-67; 50-62; 432-446, CK2_PHOSPHO_SITE 92-95; sp_Q9GZQ2_Q9GZQ2_HUMAN1.178; CK2_PHOSPHO_SITE 173-176; 238-281; 348-355, MYRISTYL 408-413;SH3DOMAIN 1.104; ASN_GLYCOSYLATION 109-112; 274-286; SH3 401-418,MYRISTYL 384-389; 229-288; 1.153; CK2_PHOSPHO_SITE 427-430; 368-374,CK2_PHOSPHO_SITE 452-455; 1.055; CK2_PHOSPHO_SITE 138-141; 45-60,PKC_PHOSPHO_SITE 341-343; 1.079; CK2_PHOSPHO_SITE 147-150; 275-300,PKC_PHOSPHO_SITE 262-264; 1.135; 387-397, 1.077; 205-212, 1.141;176-182, 1.052; 378-384, 1.046; 117-136, 1.127; 67-83, 1.127; 4-41,1.232; DEX0455_051.orf.6 N 0 - 368-374, CK2_PHOSPHO_SITE 443-446; SH3229-288; o1-474; 1.055; CK2_PHOSPHO_SITE 452-455; SH3DOMAIN 232-242;205-212, PKC_PHOSPHO_SITE 56-58; SH3DOMAIN 1.141; MYRISTYL 408-413;246-261; 348-355, CK2_PHOSPHO_SITE 63-66; PRICHEXTENSN 1.104; MYRISTYL402-407; 308-320; 93-108, CK2_PHOSPHO_SITE 147-150;sp_Q9GZQ2_Q9GZQ2_HUMAN 1.13; MYRISTYL 384-389; 238-281; 275-300,TYR_PHOSPHO_SITE 60-67; PRICHEXTENSN 1.135; ASN_GLYCOSYLATION 109-112;50-62; 45-60, MYRISTYL 337-342; PRICHEXTENSN 1.079; CK2_PHOSPHO_SITE138-141; 165-182; SH3 176-182, CK2_PHOSPHO_SITE 92-95; 232-286; 1.052;PKC_PHOSPHO_SITE 119-121; SH3DOMAIN 274-286; 401-418, CK2_PHOSPHO_SITE173-176; PRO_RICH 1.153; ASN_GLYCOSYLATION 244-247; 285-327; SH3378-384, PKC_PHOSPHO_SITE 249-251; 232-287; 1.046; CK2_PHOSPHO_SITE160-163; 67-83, PKC_PHOSPHO_SITE 138-140; 1.127; PKC_PHOSPHO_SITE341-343; 117-136, PKC_PHOSPHO_SITE 262-264; 1.127; CK2_PHOSPHO_SITE341-344; 387-397, CK2_PHOSPHO_SITE 427-430; 1.077; 4-41, 1.232; 232-239,1.134; 306-321, 1.091; 423-429, 1.071; 432-446, 1.178; 451-457, 1.113;247-261, 1.122; DEX0455_052.aa.1 N 0 - 63-79, PKC_PHOSPHO_SITE 258-260;PRO_RICH 281-323; o1-470; 1.127; CK2_PHOSPHO_SITE 423-426; PRICHEXTENSN271-296, CK2_PHOSPHO_SITE 59-62; 161-178; SH3 1.135; PKC_PHOSPHO_SITE245-247; 228-283; 383-393, PKC_PHOSPHO_SITE 52-54; PRICHEXTENSN 1.077;CK2_PHOSPHO_SITE 143-146; 304-316; 243-257, CK2_PHOSPHO_SITE 134-137;SH3DOMAIN 270-282; 1.122; CK2_PHOSPHO_SITE 88-91; SH3DOMAIN 4-37,PKC_PHOSPHO_SITE 134-136; 242-257; SH3 1.232; ASN_GLYCOSYLATION 105-108;228-282; 89-104, PKC_PHOSPHO_SITE 337-339; SH3DOMAIN 228-238; 1.13;MYRISTYL 398-403; PRICHEXTENSN 374-380, ASN_GLYCOSYLATION 240-243;46-58; SH3 225-284; 1.046; TYR_PHOSPHO_SITE 56-63;sp_Q9GZQ2_Q9GZQ2_HUMAN 41-56, MYRISTYL 333-338; 234-277; 1.079;CK2_PHOSPHO_SITE 439-442; 397-414, MYRISTYL 380-385; 1.153;PKC_PHOSPHO_SITE 115-117; 364-370, CK2_PHOSPHO_SITE 337-340; 1.055;CK2_PHOSPHO_SITE 448-451; 419-425, MYRISTYL 404-409; 1.071;CK2_PHOSPHO_SITE 169-172; 302-317, CK2_PHOSPHO_SITE 156-159; 1.091;172-178, 1.052; 447-453, 1.113; 228-235, 1.134; 344-351, 1.104, 201-208,1.141; 113-132, 1.127; 428-442, 1.178; DEX0455_052.aa.2 N 0 - 479-485,CK2_PHOSPHO_SITE 156-159; SH3DOMAIN 302-314; o1-502; 1.113;CK2_PHOSPHO_SITE 455-458; sp_Q9GZQ2_Q9GZQ2_HUMAN 260-267,CK2_PHOSPHO_SITE 59-62; 266-309; 1.134; CK2_PHOSPHO_SITE 134-137;SH3DOMAIN 223-240, PKC_PHOSPHO_SITE 290-292; 274-289; SH3 1.141;CK2_PHOSPHO_SITE 369-372; 257-316; SH3 406-412, MYRISTYL 365-370;260-314; SH3 1.046; ASN_GLYCOSYLATION 105-108; 260-315; 303-328,ASN_GLYCOSYLATION 272-275; SH3DOMAIN 260-270; 1.135; TYR_PHOSPHO_SITE56-63; PRO_RICH 376-383, PKC_PHOSPHO_SITE 277-279; 313-355; 1.104;CK2_PHOSPHO_SITE 88-91; 451-457, PKC_PHOSPHO_SITE 52-54; 1.071;CK2_PHOSPHO_SITE 143-146; 415-425, PKC_PHOSPHO_SITE 115-117; 1.077;MYRISTYL 412-417; MYRISTYL 275-289, 430-435; PKC_PHOSPHO_SITE 1.122;134-136; CK2_PHOSPHO_SITE 4-37, 169-172; MYRISTYL 436-441; 1.232;CK2_PHOSPHO_SITE 471-474; 334-349, CK2_PHOSPHO_SITE 480-483; 1.091;PKC_PHOSPHO_SITE 369-371; 63-79, 1.127; 113-132, 1.127; 396-402, 1.055;172-178, 1.052; 429-446, 1.153; 89-104, 1.13; 460-474, 1.178; 41-56,1.079; DEX0455_052.aa.3 Y 0 - 4-29, PKC_PHOSPHO_SITE 512-514; o1-548;1.211; MYRISTYL 135-140; 79-95, ASN_GLYCOSYLATION 340-343; 1.162;MYRISTYL 188-193; 56-73, PKC_PHOSPHO_SITE 41-43; 1.118; CK2_PHOSPHO_SITE36-39; 495-502, CK2_PHOSPHO_SITE 391-394; 1.134; PKC_PHOSPHO_SITE350-352; 510-519, AMIDATION 1-4; 1.1; CK2_PHOSPHO_SITE 294-297; 167-185,PKC_PHOSPHO_SITE 276-278; 1.133; MYRISTYL 212-217; 239-258,CK2_PHOSPHO_SITE 183-186; 1.131; PKC_PHOSPHO_SITE 287-289; 263-269,ASN_GLYCOSYLATION 12-15; 1.084; PKC_PHOSPHO_SITE 369-371; 99-109,CK2_PHOSPHO_SITE 74-77; 1.259; CK2_PHOSPHO_SITE 323-326; 208-214,CK2_PHOSPHO_SITE 369-372; 1.045; CAMP_PHOSPHO_SITE 174-177; 407-413,CK2_PHOSPHO_SITE 68-71; 1.052; TYR_PHOSPHO_SITE 291-298; 298-314,AMIDATION 272-275; 1.127; CK2_PHOSPHO_SITE 404-407; 134-140,PKC_PHOSPHO_SITE 177-179; 1.047; CK2_PHOSPHO_SITE 155-158; 324-339,CK2_PHOSPHO_SITE 215-218; 1.13; ASN_GLYCOSYLATION 507-510; 42-48,CK2_PHOSPHO_SITE 526-529; 1.082; CK2_PHOSPHO_SITE 378-381; 149-154,PKC_PHOSPHO_SITE 142-144; 1.041; MYRISTYL 121-126; 348-367, 1.127;525-531, 1.113; 283-291, 1.075; 113-127, 1.116; 458-475, 1.141; 229-237,1.127; DEX0455_052.aa.4 Y 0 - 78-103, MYRISTYL 2-7; SH3DOMAIN 77-89;o1-277; 1.135; PKC_PHOSPHO_SITE 16-18; PRICHEXTENSN 109-124,CK2_PHOSPHO_SITE 230-233; 170-195; 1.091; MYRISTYL 211-216; PRICHEXTENSN235-249, CK2_PHOSPHO_SITE 246-249; 112-128; SH3 1.178; MYRISTYL 205-210;35-89; 254-260, CK2_PHOSPHO_SITE 255-258; PRICHEXTENSN 1.113;CK2_PHOSPHO_SITE 144-147; 88-109; 4-19, PKC_PHOSPHO_SITE 65-67; PRO_RICH88-130; 1.169; MYRISTYL 140-145; SH3 32-91; 151-158, PKC_PHOSPHO_SITE144-146; SH3DOMAIN 35-45; 1.104; ASN_GLYCOSYLATION 47-50; SH3 35-90;181-187, CK2_PHOSPHO_SITE 16-19; sp_Q9GZQ2_Q9GZQ2_HUMAN 1.046;PKC_PHOSPHO_SITE 52-54; 41-84; 204-221, MYRISTYL 187-192; SH3DOMAIN49-64; 1.153; 190-200, 1.077; 50-64, 1.122; 226-232, 1.071; 35-42,1.134; 171-177, 1.055; DEX0455_053.aa.1 Y 1 - 73-83, ASN_GLYCOSYLATION112-115; IG_LIKE_2 153-241; i1-6; 1.16; CK2_PHOSPHO_SITE 91-94;IG_LIKE_1 tm7-29; 36-45, ASN_GLYCOSYLATION 216-219; 49-151; o30-282;1.103; CK2_PHOSPHO_SITE 151-154; 152-160, CAMP_PHOSPHO_SITE 246-249;1.069; ASN_GLYCOSYLATION 196-199; 176-186, PKC_PHOSPHO_SITE 32-34;1.162; MYRISTYL 188-193; 127-134, CK2_PHOSPHO_SITE 183-186; 1.125;PKC_PHOSPHO_SITE 207-209; 207-217, ASN_GLYCOSYLATION 190-193; 1.215;ASN_GLYCOSYLATION 160-163; 53-59, MYRISTYL 52-57; 1.066;PKC_PHOSPHO_SITE 127-129; 61-71, ASN_GLYCOSYLATION 205-208; 1.119;CK2_PHOSPHO_SITE 241-244; 248-279, PKC_PHOSPHO_SITE 134-136; 1.179;CK2_PHOSPHO_SITE 197-200; 100-123, PKC_PHOSPHO_SITE 165-167; 1.136;PKC_PHOSPHO_SITE 114-116; 165-171, ASN_GLYCOSYLATION 220-223; 1.06;MYRISTYL 126-131; 4-30, 1.146; DEX0455_053.aa.2 Y 1 - 4-39, i1-6; 1.146;tm7-29; 41-56, o30-59; 1.17; DEX0455_053.aa.3 N 0 - 177-187,ASN_GLYCOSYLATION 166-169; IG_LIKE_1 19-121; o1-252; 1.215;PKC_PHOSPHO_SITE 177-179; ig 19-102; 43-53, PKC_PHOSPHO_SITE 97-99; IG11-116; 1.16; CK2_PHOSPHO_SITE 153-156; IG_LIKE_2 123-211; 23-29, 1.1;PKC_PHOSPHO_SITE 104-106; 122-130, ASN_GLYCOSYLATION 160-163; 1.069;CK2_PHOSPHO_SITE 167-170; 146-156, ASN_GLYCOSYLATION 186-189; 1.162;CAMP_PHOSPHO_SITE 216-219; 218-249, CK2_PHOSPHO_SITE 61-64; 1.179;ASN_GLYCOSYLATION 82-85; 6-15, CK2_PHOSPHO_SITE 121-124; 1.103;PKC_PHOSPHO_SITE 84-86; 70-93, CK2_PHOSPHO_SITE 211-214; 1.136;ASN_GLYCOSYLATION 190-193; 97-104, MYRISTYL 158-163; 1.125;ASN_GLYCOSYLATION 130-133; 135-141, MYRISTYL 96-101; MYRISTYL 1.06;22-27; PKC_PHOSPHO_SITE 31-41, 135-137; ASN_GLYCOSYLATION 1.119;175-178; DEX0455_054.orf.1 N 0 - 6-13, CK2_PHOSPHO_SITE 72-75; PRO_RICH51-70; o1-155; 1.134; PKC_PHOSPHO_SITE 67-69; 145-152, AMIDATION124-127; 1.23; MYRISTYL 109-114; MYRISTYL 34-51, 79-84; CK2_PHOSPHO_SITE1.251; 89-92; 53-87, 1.163; 21-30, 1.088; 99-123, 1.205;DEX0455_054.aa.1 N 0 - 23-31, PKC_PHOSPHO_SITE 100-102;sp_P14786_KPY2_HUMAN o1-107; 1.113; MYRISTYL 94-99; 12-105; 4-20, 1.19;PKC_PHOSPHO_SITE 35-37; PK_C 3-105; 61-67, 1.089; 36-57, 1.184; 81-90,1.191; DEX0455_054.orf.2 N 0 - 99-123, AMIDATION 124-127; PRO_RICH51-70; o1-155; 1.205; CK2_PHOSPHO_SITE 89-92; 6-13, MYRISTYL 79-84;1.134; PKC_PHOSPHO_SITE 67-69; 53-87, MYRISTYL 109-114; 1.163;CK2_PHOSPHO_SITE 72-75; 145-152, 1.23; 34-51, 1.251; 21-30, 1.088;DEX0455_054.aa.2 N 0 - 28-45, MYRISTYL 27-32; PK_C 21-141; o1-143;1.179; PKC_PHOSPHO_SITE 32-34; sp_P11974_KPY1_RABIT 72-93,PKC_PHOSPHO_SITE 136-138; 1-141; 1.184; PKC_PHOSPHO_SITE 71-73; 50-56,MYRISTYL 130-135; 1.095; PKC_PHOSPHO_SITE 46-48; 117-126, 1.191; 7-14,1.1; 97-103, 1.089; 59-67, 1.113; DEX0455_055.aa.1 N 0 - MYRISTYL 52-57;o1-253; CK2_PHOSPHO_SITE 11-14; PKC_PHOSPHO_SITE 19-21; PKC_PHOSPHO_SITE207-209; CK2_PHOSPHO_SITE 9-12; PKC_PHOSPHO_SITE 164-166;CK2_PHOSPHO_SITE 7-10; CAMP_PHOSPHO_SITE 131-134; PKC_PHOSPHO_SITE130-132; PKC_PHOSPHO_SITE 245-247; CK2_PHOSPHO_SITE 243-246; AMIDATION176-179; CK2_PHOSPHO_SITE 19-22; DEX0455_055.aa.2 N 0 - 107-114,CAMP_PHOSPHO_SITE 18-21; o1-361; 1.114; CK2_PHOSPHO_SITE 12-15; 42-52,AMIDATION 348-351; 1.147; MYRISTYL 107-112; 83-97, PKC_PHOSPHO_SITE344-346; 1.14; CAMP_PHOSPHO_SITE 186-189; 70-76, MYRISTYL 311-316;1.055; CAMP_PHOSPHO_SITE 309-312; 236-242, PKC_PHOSPHO_SITE 325-327;1.115; AMIDATION 231-234; 4-11, CK2_PHOSPHO_SITE 62-65; 1.148; MYRISTYL22-27; 320-326, CK2_PHOSPHO_SITE 66-69; 1.056; ASN_GLYCOSYLATION358-361; 164-186, PKC_PHOSPHO_SITE 262-264; 1.208; AMIDATION 306-309;124-135, PKC_PHOSPHO_SITE 16-18; 1.132; CK2_PHOSPHO_SITE 74-77; 273-278,PKC_PHOSPHO_SITE 185-187; 1.03; PKC_PHOSPHO_SITE 219-221; 99-105,PKC_PHOSPHO_SITE 74-76; 1.047; CK2_PHOSPHO_SITE 319-322; 224-230,AMIDATION 339-342; 1.064; CK2_PHOSPHO_SITE 64-67; CAMP_PHOSPHO_SITE341-344; PKC_PHOSPHO_SITE 293-295; DEX0455_055.aa.3 N 0 - 28-49,AMIDATION 112-115; i1-167; 1.115; MYRISTYL 117-122; 126-137,PKC_PHOSPHO_SITE 25-27; 1.056; PKC_PHOSPHO_SITE 131-133; 68-84,PKC_PHOSPHO_SITE 150-152; 1.038; AMIDATION 145-148; 4-10,CAMP_PHOSPHO_SITE 147-150; 1.009; CK2_PHOSPHO_SITE 125-128; 12-19,PKC_PHOSPHO_SITE 99-101; 1.035; AMIDATION 37-40; 60-66,CAMP_PHOSPHO_SITE 115-118; 1.026; AMIDATION 154-157; PKC_PHOSPHO_SITE68-70; ASN_GLYCOSYLATION 164-167; DEX0455_056.orf.1 N 0 - 53-59,ASN_GLYCOSYLATION 199-202; o1-636; 1.147; MYRISTYL 65-70; MYRISTYL401-411, 451-456; CK2_PHOSPHO_SITE 1.092; 221-224; ASN_GLYCOSYLATION4-10, 454-457; CK2_PHOSPHO_SITE 1.067; 574-577; CK2_PHOSPHO_SITE592-633, 115-118; MYRISTYL 531-536; 1.179; CK2_PHOSPHO_SITE 347-350;218-253, CK2_PHOSPHO_SITE 137-140; 1.106; CK2_PHOSPHO_SITE 308-311;474-480, CK2_PHOSPHO_SITE 301-304; 1.058; MYRISTYL 336-341; MYRISTYL95-136, 154-159; PKC_PHOSPHO_SITE 1.207; 201-203; MYRISTYL 231-236;440-448, CK2_PHOSPHO_SITE 525-528; 1.082; ASN_GLYCOSYLATION 415-418;354-372, MYRISTYL 206-211; 1.185; PKC_PHOSPHO_SITE 565-567; 165-203,PKC_PHOSPHO_SITE 286-288; 1.177; TYR_PHOSPHO_SITE 351-357; 66-74,MYRISTYL 60-65; 1.083; TYR_PHOSPHO_SITE 421-428; 429-437, AMIDATION20-23; 1.111; CK2_PHOSPHO_SITE 70-73; 142-148, MYRISTYL 63-68; 1.091;PKC_PHOSPHO_SITE 70-72; 153-163, CK2_PHOSPHO_SITE 293-296; 1.075;MYRISTYL 588-593; MYRISTYL 274-285, 51-56; CAMP_PHOSPHO_SITE 1.132;23-26; ASN_GLYCOSYLATION 374-386, 548-551; CK2_PHOSPHO_SITE 1.187;35-38; MYRISTYL 4-9; 578-584, MYRISTYL 11-16; 1.107; CK2_PHOSPHO_SITE235-238; 530-574, CK2_PHOSPHO_SITE 286-289; 1.129; MYRISTYL 49-54;460-466, 1.147; 76-83, 1.118; 490-518, 1.111; 259-265, 1.052; 290-302,1.163; 309-325, 1.128; DEX0455_056.aa.1 N 0 - 38-44, CK2_PHOSPHO_SITE559-562; o1-870; 1.147; CK2_PHOSPHO_SITE 122-125; 386-396, MYRISTYL659-664; MYRISTYL 1.092; 36-41; MYRISTYL 34-39; 690-699,PKC_PHOSPHO_SITE 271-273; 1.137; CK2_PHOSPHO_SITE 510-513; 679-688,MYRISTYL 45-50; 1.065; TYR_PHOSPHO_SITE 406-413; 339-357,CK2_PHOSPHO_SITE 206-209; 1.185; MYRISTYL 834-839; 259-270,PKC_PHOSPHO_SITE 664-666; 1.132; CK2_PHOSPHO_SITE 332-335; 634-652,ASN_GLYCOSYLATION 533-536; 1.134; MYRISTYL 436-441; MYRISTYL 515-559,139-144; MYRISTYL 191-196; 1.129; MYRISTYL 573-578; 51-59,PKC_PHOSPHO_SITE 550-552; 1.083; CK2_PHOSPHO_SITE 220-223; 425-433,PKC_PHOSPHO_SITE 762-764; 1.082; CK2_PHOSPHO_SITE 100-103; 294-310,CK2_PHOSPHO_SITE 824-827; 1.128; CK2_PHOSPHO_SITE 640-643; 445-451,MYRISTYL 321-326; 1.147; PKC_PHOSPHO_SITE 55-57; 275-287,PKC_PHOSPHO_SITE 186-188; 1.163; CK2_PHOSPHO_SITE 20-23; 244-250,CK2_PHOSPHO_SITE 286-289; 1.052; MYRISTYL 216-221; 763-796,CK2_PHOSPHO_SITE 278-281; 1.144; PKC_PHOSPHO_SITE 842-844; 459-465,ASN_GLYCOSYLATION 184-187; 1.058; CAMP_PHOSPHO_SITE 748-751; 827-844,MYRISTYL 516-521; MYRISTYL 1.127; 50-55; TYR_PHOSPHO_SITE 150-188,336-342; PKC_PHOSPHO_SITE 1.177; 756-758; ASN_GLYCOSYLATION 414-422,439-442; ASN_GLYCOSYLATION 1.111; 400-403; AMIDATION 5-8; 739-754,PKC_PHOSPHO_SITE 824-826; 1.163; CAMP_PHOSPHO_SITE 8-11; 659-664,CK2_PHOSPHO_SITE 293-296; 1.038; CK2_PHOSPHO_SITE 55-58; 707-723,CK2_PHOSPHO_SITE 271-274; 1.101; MYRISTYL 48-53; 359-371, 1.187;798-805, 1.037; 203-238, 1.106; 80-121, 1.207; 563-569, 1.107; 851-867,1.148; 577-629, 1.179; 475-503, 1.111; 127-133, 1.091; 138-148, 1.075;61-68, 1.118; 666-676, 1.164; DEX0455_056.aa.2 N 0 - 244-250,CAMP_PHOSPHO_SITE 738-741; o1-791; 1.052; PKC_PHOSPHO_SITE 55-57; 51-59,CK2_PHOSPHO_SITE 220-223; 1.083; CK2_PHOSPHO_SITE 100-103; 339-357,CK2_PHOSPHO_SITE 122-125; 1.185; CK2_PHOSPHO_SITE 271-274; 577-619,CK2_PHOSPHO_SITE 286-289; 1.179; CAMP_PHOSPHO_SITE 8-11; 772-788,PKC_PHOSPHO_SITE 654-656; 1.148; MYRISTYL 191-196; MYRISTYL 669-678,516-521; CK2_PHOSPHO_SITE 1.065; 510-513; MYRISTYL 36-41; 138-148,PKC_PHOSPHO_SITE 763-765; 1.075; CK2_PHOSPHO_SITE 630-633; 656-666,MYRISTYL 321-326; 1.164; CK2_PHOSPHO_SITE 332-335; 294-310,PKC_PHOSPHO_SITE 271-273; 1.128; MYRISTYL 216-221; 475-503,PKC_PHOSPHO_SITE 186-188; 1.111; CK2_PHOSPHO_SITE 293-296; 515-559,MYRISTYL 139-144; 1.129; ASN_GLYCOSYLATION 439-442; 459-465, MYRISTYL573-578; 1.058; AMIDATION 5-8; MYRISTYL 697-713, 50-55; PKC_PHOSPHO_SITE1.101; 752-754; PKC_PHOSPHO_SITE 386-396, 550-552; ASN_GLYCOSYLATION1.092; 533-536; TYR_PHOSPHO_SITE 624-642, 406-413; MYRISTYL 48-53;1.134; PKC_PHOSPHO_SITE 746-748; 445-451, CK2_PHOSPHO_SITE 559-562;1.147; ASN_GLYCOSYLATION 400-403; 127-133, MYRISTYL 34-39; MYRISTYL1.091; 436-441; CK2_PHOSPHO_SITE 680-689, 278-281; CK2_PHOSPHO_SITE1.137; 206-209; MYRISTYL 649-654; 38-44, CK2_PHOSPHO_SITE 20-23; 1.147;ASN_GLYCOSYLATION 184-187; 359-371, TYR_PHOSPHO_SITE 336-342; 1.187;MYRISTYL 755-760; 259-270, CK2_PHOSPHO_SITE 55-58; 1.132; MYRISTYL45-50; 414-422, 1.111; 563-569, 1.107; 753-765, 1.127; 203-238, 1.106;425-433, 1.082; 729-744, 1.163; 275-287, 1.163; 150-188, 1.177; 80-121,1.207; 61-68, 1.118; 649-654, 1.038; DEX0455_057.orf.1 N 0 - 97-119,PKC_PHOSPHO_SITE 3-5; EF_HAND_2 25-101; o1-122; 1.114; ASN_GLYCOSYLATION48-51; S100_CABP 30-41, CK2_PHOSPHO_SITE 25-28; 80-101; EFh 76-104;1.138; PKC_PHOSPHO_SITE 27-29; sp_P31949_S111_HUMAN 4-13,CK2_PHOSPHO_SITE 23-26; 25-94; 1.125; PKC_PHOSPHO_SITE 118-120; S_10027-70; MYRISTYL 103-108; efhand 76-104; CK2_PHOSPHO_SITE 12-15;sp_O93395_O93395_SALFO CK2_PHOSPHO_SITE 86-89; 44-98; CK2_PHOSPHO_SITE52-55; EF_HAND 85-97; DEX0455_057.aa.1 N 0 - 78-89, ASN_GLYCOSYLATION96-99; sp_P31949_S111_HUMAN o1-170; 1.138; CK2_PHOSPHO_SITE 71-74;73-142; 145-167, PKC_PHOSPHO_SITE 55-57; EF_HAND 133-145; 1.114;CK2_PHOSPHO_SITE 43-46; S100_CABP 4-38, PKC_PHOSPHO_SITE 75-77; 128-149;1.16; CK2_PHOSPHO_SITE 134-137; sp_O93395_O93395_SALFO PKC_PHOSPHO_SITE166-168; 92-146; CK2_PHOSPHO_SITE 100-103; efhand 124-152; MYRISTYL151-156; EFh 124-152; CK2_PHOSPHO_SITE 73-76; S_100 75-118;PKC_PHOSPHO_SITE 58-60; EF_HAND_2 73-149; CK2_PHOSPHO_SITE 6-9;DEX0455_057.aa.2 N 0 - 66-88, CK2_PHOSPHO_SITE 55-58; EFh 45-73; o1-91;1.114; ASN_GLYCOSYLATION 17-20; efhand 45-73; 4-11, PKC_PHOSPHO_SITE87-89; S100_CABP 49-70; 1.134; CK2_PHOSPHO_SITE 21-24; S_100 3-39;MYRISTYL 72-77; EF_HAND 54-66; sp_P31949_S111_HUMAN 9-63; EF_HAND_219-70; sp_O93395_O93395_SALFO 13-67; DEX0455_058.orf.1 N 1 - 4-25,CK2_PHOSPHO_SITE 23-26; o1-14; 1.178; MYRISTYL 27-32; tm15-37; 27-63,i38-66; 1.191; DEX0455_058.aa.1 N 0 - 24-32, TYR_PHOSPHO_SITE 12-18;o1-65; 1.155; ASN_GLYCOSYLATION 59-62; 36-54, CK2_PHOSPHO_SITE 6-9;1.162; 14-22, 1.084; DEX0455_059.orf.1 N 0 - 104-122, PKC_PHOSPHO_SITE80-82; o1-363; 1.145; CK2_PHOSPHO_SITE 28-31; 261-268, PKC_PHOSPHO_SITE281-283; 1.085; CAMP_PHOSPHO_SITE 105-108; 11-21, MYRISTYL 47-52; 1.113;CAMP_PHOSPHO_SITE 77-80; 341-351, PKC_PHOSPHO_SITE 103-105; 1.191;MYRISTYL 335-340; 125-159, PKC_PHOSPHO_SITE 206-208; 1.118;PKC_PHOSPHO_SITE 76-78; 178-212, MYRISTYL 304-309; MYRISTYL 1.171;71-76; PKC_PHOSPHO_SITE 69-77, 28-30; PKC_PHOSPHO_SITE 8-10; 1.128;CK2_PHOSPHO_SITE 17-20; 315-330, PKC_PHOSPHO_SITE 62-64; 1.192;CK2_PHOSPHO_SITE 237-240; 270-275, 1.039; 235-248, 1.131; 281-289,1.116; 353-360, 1.134; 85-102, 1.157; 295-305, 1.07; 225-232, 1.131;DEX0455_059.aa.1 N 0 - 38-67, PKC_PHOSPHO_SITE 25-27; o1-116; 1.204;PKC_PHOSPHO_SITE 58-60; 28-34, AMIDATION 16-19; 1.111; CK2_PHOSPHO_SITE5-8; 12-23, PKC_PHOSPHO_SITE 45-47; 1.084; 71-113, 1.168;DEX0455_059.orf.2 N 0 - 118-133, MYRISTYL 107-112; o1-166; 1.192;CK2_PHOSPHO_SITE 40-43; 16-26, MYRISTYL 138-143; 1.124; PKC_PHOSPHO_SITE84-86; 98-108, 1.07; 144-154, 1.191; 64-71, 1.085; 7-13, 1.026; 38-51,1.131; 84-92, 1.116; 28-35, 1.122; 156-163, 1.134; 73-78, 1.039;DEX0455_060.aa.1 Y 0 - 115-122, MYRISTYL 76-81; AMIDATION BTG_1 124-144;o1-207; 1.108; 79-82; PKC_PHOSPHO_SITE ANTIPRLFBTG1 149-187, 42-44;MYRISTYL 34-39; 173-202; 1.215; MYRISTYL 41-46; Anti_proliferat 193-199,PKC_PHOSPHO_SITE 24-26; 83-207; BTG_2 1.122; MYRISTYL 75-80; 170-189;btg1 4-26, 83-190; 1.251; ANTIPRLFBTG1 138-145, 88-112; 1.131;ANTIPRLFBTG1 43-56, 113-142; 1.102; 87-101, 1.175; DEX0455_061.aa.1 N0 - 173-179, MYRISTYL 57-62; RA 203-293; o1-352; 1.031; CK2_PHOSPHO_SITE22-25; RA_DOMAIN 205-293; 264-290, MYRISTYL 133-138; RA 203-293; 1.129;CK2_PHOSPHO_SITE 150-153; 181-187, PKC_PHOSPHO_SITE 178-180; 1.04;ASN_GLYCOSYLATION 134-137; 138-148, MYRISTYL 43-48; AMIDATION 1.114;10-13; CAMP_PHOSPHO_SITE 36-68, 119-122; CK2_PHOSPHO_SITE 1.256;314-317; ASN_GLYCOSYLATION 4-10, 1.15; 225-228; TYR_PHOSPHO_SITE108-113, 263-269; PKC_PHOSPHO_SITE 1.105; 331-333; CK2_PHOSPHO_SITE230-241, 170-173; MYRISTYL 217-222; 1.187; 120-128, 1.086; 249-257,1.172; 344-349, 1.095; 14-20, 1.171; 208-225, 1.103; 333-340, 1.068;81-91, 1.111; 292-319, 1.15; DEX0455_061.aa.2 N 0 - 230-241,ASN_GLYCOSYLATION 134-137; RA 203-260; o1-261; 1.187; MYRISTYL 43-48;RA_DOMAIN 205-261; 108-113, CAMP_PHOSPHO_SITE 119-122; 1.105; MYRISTYL57-62; 173-179, CK2_PHOSPHO_SITE 150-153; 1.031; PKC_PHOSPHO_SITE178-180; 208-225, AMIDATION 10-13; 1.103; CK2_PHOSPHO_SITE 22-25; 36-68,MYRISTYL 217-222; 1.256; ASN_GLYCOSYLATION 225-228; 81-91, MYRISTYL133-138; 1.111; CK2_PHOSPHO_SITE 170-173; 249-258, 1.172; 138-148,1.114; 120-128, 1.086; 4-10, 1.15; 14-20, 1.171; 181-187, 1.04;DEX0455_061.aa.3 N 0 - 181-187, CK2_PHOSPHO_SITE 22-25; RA 203-269;o1-269; 1.04; CK2_PHOSPHO_SITE 258-261; RA_DOMAIN 205-269; 36-68,MYRISTYL 133-138; 1.256; CK2_PHOSPHO_SITE 170-173; 120-128,CK2_PHOSPHO_SITE 150-153; 1.086; ASN_GLYCOSYLATION 225-228; 230-241,AMIDATION 10-13; MYRISTYL 1.187; 217-222; ASN_GLYCOSYLATION 14-20,134-137; MYRISTYL 57-62; 1.171; PKC_PHOSPHO_SITE 178-180; 4-10, 1.15;MYRISTYL 43-48; 173-179, CAMP_PHOSPHO_SITE 119-122; 1.031; 108-113,1.105; 81-91, 1.111; 138-148, 1.114; 208-225, 1.103; 249-257, 1.172;DEX0455_061.aa.4 Y 0 - 4-31, ASN_GLYCOSYLATION 51-54; o1-133; 1.159;PKC_PHOSPHO_SITE 77-79; 61-129, 1.207; 41-58, 1.181; DEX0455_061.orf.5 N0 - 92-130, CK2_PHOSPHO_SITE 51-54; o1-163; 1.205; MYRISTYL 17-22;56-85, PKC_PHOSPHO_SITE 5-7; 1.181; CK2_PHOSPHO_SITE 47-50; 147-160,MYRISTYL 143-148; MYRISTYL 1.134; 144-149; MYRISTYL 139-144; 4-11,1.118; 32-52, 1.22; DEX0455_062.aa.1 Y 0 - 395-401, CK2_PHOSPHO_SITE22-25; thiored 24-132; o1-491; 1.032; MYRISTYL 140-145; THIOREDOXIN47-65; 180-196, CK2_PHOSPHO_SITE 290-293; pdi_dom 1.118;CK2_PHOSPHO_SITE 315-318; 165-269; 403-409, CK2_PHOSPHO_SITE 343-346;THIOREDOXIN 1.077; PKC_PHOSPHO_SITE 157-159; 189-198; 121-138, MYRISTYL422-427; THIOREDOXIN 46-54; 1.121; CK2_PHOSPHO_SITE 257-260;THIOREDOXIN_2_2 214-232, MYRISTYL 454-459; 161-284; 1.143;CK2_PHOSPHO_SITE 405-408; THIOREDOXIN 4-31, PKC_PHOSPHO_SITE 100-102;233-244; 1.234; CK2_PHOSPHO_SITE 158-161; THIOREDOXIN_2_1 431-463,CK2_PHOSPHO_SITE 248-251; 26-137; thiored 1.191; MYRISTYL 401-406;159-270; 259-269, CK2_PHOSPHO_SITE 375-378; pdi_dom 30-131; 1.1;MYRISTYL 90-95; THIOREDOXIN 86-103, PKC_PHOSPHO_SITE 464-466; 182-200;1.07; PKC_PHOSPHO_SITE 106-108; 292-308, MYRISTYL 116-121; 1.304;PKC_PHOSPHO_SITE 158-160; 465-481, MYRISTYL 105-110; 1.149;PKC_PHOSPHO_SITE 148-150; 69-84, 1.2; MYRISTYL 79-84; MYRISTYL 159-165,19-24; MYRISTYL 458-463; 1.052; MYRISTYL 144-149; 38-61,PKC_PHOSPHO_SITE 239-241; 1.134; MYRISTYL 7-12; 201-207,CK2_PHOSPHO_SITE 23-26; 1.072; 275-281, 1.087; 369-375, 1.067; 422-429,1.117; 316-326, 1.166; 172-178, 1.087;

Example 1b Sequence Alignment Support

Alignments between previously identified sequences and splice variantsequences are performed to confirm unique portions of splice variantnucleic acid and amino acid sequences. The alignments are done using theNeedle program in the European Molecular Biology Open Software Suite(EMBOSS) version 2.2.0 available at www.emboss.org from EMBnet(http://www.embnet.org). Default settings are used unless otherwisenoted. The Needle program in EMBOSS implements the Needleman-Wunschalgorithm. Needleman, S. B., Wunsch, C. D., J. Mol. Biol. 48:443453(1970).

It is well know to those skilled in the art that implication ofalignment algorithms by various programs may result in minor changes inthe generated output. These changes include but are not limited to:alignment scores (percent identity, similarity, and gap), display ofnonaligned flanking sequence regions, and number assignment to residues.These minor changes in the output of an alignment do not alter thephysical characteristics of the sequences or the differences between thesequences, e.g. regions of homology, insertions, or deletions.

Example 1c RT-PCR Analysis

To detect the presence and tissue distribution of a particular splicevariant Reverse Transcription-Polymerase Chain Reaction (RT-PCR) isperformed using cDNA generated from a panel of tissue RNAs. See, e.g.,Sambrook et al., Molecular Cloning: A Laboratory Manual, 2d ed., ColdSpring Harbor Laboratory Press (1989) and; Kawasaki E S et al., PNAS85(15):5698 (1988). Total RNA is extracted from a variety of tissues andfirst strand cDNA is prepared with reverse transcriptase (RT). Eachpanel includes 23 cDNAs from five cancer types (lung, ovary, breast,colon, and prostate) and normal samples of testis, placenta and fetalbrain. Each cancer set is composed of three cancer cDNAs from differentdonors and one normal pooled sample. Using a standard enzyme kit from BDBioscience Clontech (Mountain View, Calif.), the target transcript isdetected with sequence-specific primers designed to only amplify theparticular splice variant. The PCR reaction is run on the GeneAmp PCRsystem 9700 (Applied Biosystem, Foster City, Calif.) thermocycler underoptimal conditions. One of ordinary skill can design appropriate primersand determine optimal conditions. The amplified product is resolved onan agarose gel to detect a band of equivalent size to the predictedRT-PCR product. A band indicated the presence of the splice variant in asample. The relation of the amplified product to the splice variant wassubsequently confirmed by DNA sequencing.

After subcloning, all positively screened clones are sequence verified.The DNA sequence verification results show the splice variant containsthe predicted sequence differences in comparison with the referencesequence.

Results for RT-PCR analysis in the table below include the sequence DEXID, Lead Name, Cancer Tissue(s) the transcript was detected in, NormalTissue(s) the transcript was detected in, the predicted length of theRT-PCR product, and the confirmed Length of the RT-PCR product. LeadCancer Normal Predicted Confirmed DEX ID Name Tissue(s) Tissue(s) LengthLength DEX0455_019.nt.1 Ovr224 Lung, Placenta, 334 bp 334 bp Ovary,Fetal brain Colon, Prostate DEX0455_034.nt.1, Ovr223 Lung, 448 bp 894 bpDEX0455_034.nt.2 Ovary, (exon Breast, insertion) Colon DEX0455_034.nt.3Ovr223v1 Lung, Lung, 385 bp 385 bp Ovary, Breast, Breast, Colon, Colon,Prostate, Prostate Placenta DEX0455_034.nt.4 Ovr223v2 Lung, Lung, 491 bp491 bp Ovary, Breast, Breast, Colon, Colon, Prostate, Prostate PlacentaDEX0455_037.nt.6 Ovr229 Ovary, Prostate 390 bp 387 bp ProstateDEX0455_037.nt.7 Ovr227 Prostate Placenta 257 bp 256 bp DEX0455_049.nt.1Ovr232 Lung, Breast 134 bp 134 bp Ovary, Breast, Colon DEX0455_049.nt.2Ovr232v1 Lung, Ovary, 345 bp 345 bp Ovary, Breast Breast, Colon,Prostate DEX0455_049.nt.3 Ovr232v2 Lung, Lung, Ovary, 334 bp 334 bpOvary, Breast, Breast, Colon, Colon, Prostate Prostate DEX0455_049.nt.4Ovr232v3 Colon Breast 254 bp 254 bp DEX0455_053.nt.2 Ovr110V1 Ovary,Breast 383 bp 383 bp Breast, Prostate

RT-PCR results confirm the presence SEQ ID NO: 1-128 in biologic samplesand distinguish between related transcripts.

Example 1d Secretion Assay

To determine if a protein encoded by a splice variant is secreted fromcells a secretion assay is preformed. A pcDNA3.1 clone containing thegene transcript which encodes the variant protein is transfected into293T cells using the Superfect transfection reagent (Qiagen, ValenciaCalif.). Transfected cells are incubated for 28 hours before the mediais collected and immediately spun down to remove any detached cells. Theadherent cells are solubilized with lysis buffer (1% NP40, 10 mM sodiumphosphate pH 7.0, and 0.15M NaCl). The lysed cells are collected andspun down and the supernatant extracted as cell lysate. Westernimmunoblot is carried out in the following manner: 15 μl of the celllysate and media are run on 4-12% NuPage Bis-Tris gel (Invitrogen,Carlsbad Calif.), and blotted onto a PVDF membrane (Invitrogen, CarlsbadCalif.). The blot is incubated with a polyclonal primary antibody whichbinds to the variant protein (Imgenex, San Diego Calif.) and polyclonalgoat anti-rabbit-peroxidase secondary antibody (Sigma-Aldrich, St. LouisMo.). The blot is developed with the ECL Plus chemiluminescent detectionreagent (Amersham BioSciences, Piscataway N.J.).

Secretion assay results are indicative of SEQ ID NO: 129-295 being adiagnostic marker and/or therapeutic target for cancer.

Example 2a Gene Expression Analysis

Custom Microarray Experiment—Cancer

Custom oligonucleotide microarrays were provided by AgilentTechnologies, Inc. (Palo Alto, Calif.). The microarrays were fabricatedby Agilent using their technology for the in-situ synthesis of 60meroligonucleotides (Hughes, et al. 2001, Nature Biotechnology 19:342-347).The 60mer microarray probes were designed by Agilent, from genesequences provided by diaDexus, using Agilent proprietary algorithms.Whenever possible two different 60mers were designed for each gene ofinterest

All microarray experiments were two-color experiments and were preformedusing Agilent-recommended protocols and reagents. Briefly, eachmicroarray was hybridized with cRNAs synthesized from RNA (total RNA forovarian and prostate, polyA+RNA for lung, breast and colon samples),isolated from cancer and normal tissues, labeled with fluorescent dyesCyanine3 (Cy3) or Cyanine5 (Cy5) (NEN Life Science Products, Inc.,Boston, Mass.) using a linear amplification method (Agilent). In eachexperiment the experimental sample was RNA isolated from cancer tissuefrom a single individual and the reference sample was a pool of RNAisolated from normal tissues of the same organ as the cancerous tissue(i.e. normal ovarian tissue in experiments with ovarian cancer samples).Hybridizations were carried out at 60° C., overnight using Agilentin-situ hybridization buffer. Following washing, arrays were scannedwith a GenePix 4000B Microarray Scanner (Axon Instruments, Inc., UnionCity, Calif.). The resulting images were analyzed with GenePix Pro 3.0Microarray Acquisition and Analysis Software (Axon).

Data normalization and expression profiling were done with Expressionistsoftware from GeneData Inc. (Daly City, Calif./Basel, Switzerland). Geneexpression analysis was performed using only experiments that metcertain quality criteria. The quality criteria that experiments mustmeet are a combination of evaluations performed by the Expressionistsoftware and evaluations performed manually using raw and normalizeddata. To evaluate raw data quality, detection limits (the mean signalfor a replicated negative control +2 Standard Deviations (SD)) for eachchannel were calculated. The detection limit is a measure ofnon-specific hybridization. Acceptable detection limits were defined foreach dye (<80 for Cy5 and <150 for Cy3). Arrays with poor detectionlimits in one or both channels were not analyzed and the experimentswere repeated. To evaluate normalized data quality, positive controlelements included in the array were utilized. These array featuresshould have a mean ratio of 1 (no differential expression). If thesefeatures have a mean ratio of greater than 1.5-fold up or down, theexperiments were not analyzed further and were repeated. In addition totraditional scatter plots demonstrating the distribution of signal ineach experiment, the Expressionist software also has minimumthresholding criteria that employ user defined parameters to identifyquality data. These thresholds include two distinct qualitymeasurements: 1) minimum area percentage, which is a measure of theintegrity of each spot and 2) signal to noise ratio, which ensures thatthe signal being measured is significantly above any background(nonspecific) signal present. Only those features that met the thresholdcriteria were included in the filtering and analyses carried out byExpressionist. The thresholding settings employed require a minimum areapercentage of 60% [(% pixels>background+2SD)−(% pixels saturated)], anda minimum signal to noise ratio of 2.0 in both channels. By thesecriteria, very low expressors, saturated features and spots withabnormally high local background were not included in analysis.

Relative expression data was collected from Expressionist based onfiltering and clustering analyses. Up-regulated genes were identifiedusing criteria for the percentage of experiments in which the gene isup-regulated by at least 2-fold. In general, up-regulation in ˜30% ofsamples tested was used as a cutoff for filtering.

Two microarray experiments were preformed for each normal and cancertissue pair. The tissue specific Array Chip for each cancer tissue is aunique microarray specific to that tissue and cancer. The Multi-CancerArray Chip is a universal microarray that was hybridized with samplesfrom each of the cancers (ovarian, breast, colon, lung, and prostate).See the description below for the experiments specific to the differentcancers.

Microarray Experiments and Data Tables

Ovarian Cancer Chips

For ovarian cancer two different chip designs were evaluated withoverlapping sets of a total of 19 samples, comparing the expressionpatterns of ovarian cancer derived total RNA to total RNA isolated froma pool of 9 normal ovarian tissues. For the Multi-Cancer Array Chip, all19 samples (14 invasive carcinomas, 5 low malignant potential sampleswere analyzed and for the Ovarian Array Chip, a subset of 17 of thesesamples (13 invasive carcinomas, 4 low malignant potential samples) wereassessed.

The results for the statistically significant up-regulated genes on theOvarian Array Chip are shown in Table 1. The results for theMulti-Cancer Array Chip are shown in Table 2. The first two columns ofeach table contain information about the sequence itself (DEX ID, OligoName), the next columns show the results obtained for all (“ALL”)ovarian cancer samples, invasive carcinomas (“INV”) and low malignantpotential (“LMP”) samples. ‘% up’ indicates the percentage of allexperiments in which up-regulation of at least 2-fold was observed (n=9for the Multi-Cancer Array Chip, n=17 for the Ovarian Array Chip), ‘%valid up’ indicates the percentage of experiments with valid expressionvalues in which up-regulation of at least 2-fold was observed. TABLE 1Ovr Ovr Ovr ALL Ovr ALL INV Ovr INV LMP Ovr LMP Oligo % up % valid % up% valid % up % valid DEX ID Name n = 17 up n = 17 n = 13 up n = 13 n = 4up n = 4 DEX0455_001.nt.1 34930.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_001.nt.1 34930.02 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_002.nt.121553.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_002.nt.1 21553.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_002.nt.1 21577.01 17.6 20.0 15.4 16.7 25.0 33.3DEX0455_002.nt.1 21577.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_003.nt.117466.01 11.8 11.8 7.7 7.7 25.0 25.0 DEX0455_003.nt.1 17466.02 11.8 11.87.7 7.7 25.0 25.0 DEX0455_005.nt.1 20619.01 23.5 25.0 23.1 23.1 25.033.3 DEX0455_005.nt.1 20619.02 17.6 20.0 15.4 16.7 25.0 33.3DEX0455_005.nt.1 24874.01 23.5 25.0 23.1 25.0 25.0 25.0 DEX0455_005.nt.124874.02 29.4 31.2 23.1 25.0 50.0 50.0 DEX0455_005.nt.2 20619.01 23.525.0 23.1 23.1 25.0 33.3 DEX0455_005.nt.2 20619.02 17.6 20.0 15.4 16.725.0 33.3 DEX0455_005.nt.2 24874.01 23.5 25.0 23.1 25.0 25.0 25.0DEX0455_005.nt.2 24874.02 29.4 31.2 23.1 25.0 50.0 50.0 DEX0455_007.nt.130109.01 41.2 46.7 30.8 33.3 75.0 100.0 DEX0455_007.nt.1 30109.02 35.340.0 23.1 27.3 75.0 75.0 DEX0455_008.nt.1 18508.01 23.5 44.4 30.8 44.40.0 0.0 DEX0455_008.nt.1 18508.02 17.6 23.1 23.1 30.0 0.0 0.0DEX0455_008.nt.1 22387.01 35.3 54.5 46.2 66.7 0.0 0.0 DEX0455_008.nt.122387.02 41.2 43.8 53.8 58.3 0.0 0.0 DEX0455_009.nt.1 9720.01 47.1 47.138.5 38.5 75.0 75.0 DEX0455_009.nt.1 9720.02 52.9 52.9 46.2 46.2 75.075.0 DEX0455_010.nt.1 20627.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_010.nt.1 20627.02 23.5 25.0 23.1 25.0 25.0 25.0 DEX0455_010.nt.121675.01 11.8 11.8 15.4 15.4 0.0 0.0 DEX0455_010.nt.1 21675.02 11.8 11.815.4 15.4 0.0 0.0 DEX0455_010.nt.2 21675.01 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_010.nt.2 21675.02 11.8 11.8 15.4 15.4 0.0 0.0 DEX0455_013.nt.19838.01 35.3 42.9 38.5 45.5 25.0 33.3 DEX0455_013.nt.1 9838.02 35.3 37.538.5 38.5 25.0 33.3 DEX0455_013.nt.2 9838.01 35.3 42.9 38.5 45.5 25.033.3 DEX0455_013.nt.2 9838.02 35.3 37.5 38.5 38.5 25.0 33.3DEX0455_014.nt.1 10624.01 17.6 50.0 15.4 50.0 25.0 50.0 DEX0455_014.nt.110624.02 17.6 50.0 7.7 33.3 50.0 66.7 DEX0455_014.nt.1 14604.01 0.0 0.00.0 0.0 0.0 0.0 DEX0455_014.nt.1 14604.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_015.nt.1 19518.01 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_015.nt.119518.02 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_016.nt.1 23734.01 5.9 6.27.7 7.7 0.0 0.0 DEX0455_016.nt.1 23734.02 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_018.nt.1 21571.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_018.nt.121571.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_018.nt.1 21575.01 41.2 41.246.2 46.2 25.0 25.0 DEX0455_018.nt.1 21575.02 41.2 41.2 46.2 46.2 25.025.0 DEX0455_018.nt.1 21609.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_018.nt.121609.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_018.nt.2 21575.01 41.2 41.246.2 46.2 25.0 25.0 DEX0455_018.nt.2 21575.02 41.2 41.2 46.2 46.2 25.025.0 DEX0455_019.nt.1 20669.01 35.3 42.9 46.2 50.0 0.0 0.0DEX0455_019.nt.1 20669.02 35.3 46.2 46.2 50.0 0.0 0.0 DEX0455_021.nt.121433.01 64.7 64.7 61.5 61.5 75.0 75.0 DEX0455_021.nt.1 21433.02 64.764.7 61.5 61.5 75.0 75.0 DEX0455_021.nt.1 21469.01 70.6 70.6 61.5 61.5100.0 100.0 DEX0455_021.nt.1 21469.02 82.4 82.4 76.9 76.9 100.0 100.0DEX0455_021.nt.1 21475.01 58.8 58.8 53.8 53.8 75.0 75.0 DEX0455_021.nt.121475.02 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_021.nt.1 23780.01 47.147.1 46.2 46.2 50.0 50.0 DEX0455_021.nt.1 23780.02 41.2 50.0 46.2 54.525.0 33.3 DEX0455_021.nt.2 21433.01 64.7 64.7 61.5 61.5 75.0 75.0DEX0455_021.nt.2 21433.02 64.7 64.7 61.5 61.5 75.0 75.0 DEX0455_021.nt.221469.01 70.6 70.6 61.5 61.5 100.0 100.0 DEX0455_021.nt.2 21469.02 82.482.4 76.9 76.9 100.0 100.0 DEX0455_021.nt.2 21475.01 58.8 58.8 53.8 53.875.0 75.0 DEX0455_021.nt.2 21475.02 52.9 52.9 53.8 53.8 50.0 50.0DEX0455_021.nt.2 23780.01 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_021.nt.223780.02 41.2 50.0 46.2 54.5 25.0 33.3 DEX0455_021.nt.3 21433.01 64.764.7 61.5 61.5 75.0 75.0 DEX0455_021.nt.3 21433.02 64.7 64.7 61.5 61.575.0 75.0 DEX0455_021.nt.3 21469.01 70.6 70.6 61.5 61.5 100.0 100.0DEX0455_021.nt.3 21469.02 82.4 82.4 76.9 76.9 100.0 100.0DEX0455_021.nt.3 21475.01 58.8 58.8 53.8 53.8 75.0 75.0 DEX0455_021.nt.321475.02 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_021.nt.3 23780.01 47.147.1 46.2 46.2 50.0 50.0 DEX0455_021.nt.3 23780.02 41.2 50.0 46.2 54.525.0 33.3 DEX0455_021.nt.4 21433.01 64.7 64.7 61.5 61.5 75.0 75.0DEX0455_021.nt.4 21433.02 64.7 64.7 61.5 61.5 75.0 75.0 DEX0455_021.nt.421469.01 70.6 70.6 61.5 61.5 100.0 100.0 DEX0455_021.nt.4 21469.02 82.482.4 76.9 76.9 100.0 100.0 DEX0455_021.nt.4 21475.01 58.8 58.8 53.8 53.875.0 75.0 DEX0455_021.nt.4 21475.02 52.9 52.9 53.8 53.8 50.0 50.0DEX0455_021.nt.4 23780.01 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_021.nt.423780.02 41.2 50.0 46.2 54.5 25.0 33.3 DEX0455_022.nt.1 9920.01 23.523.5 30.8 30.8 0.0 0.0 DEX0455_022.nt.1 9920.02 23.5 23.5 30.8 30.8 0.00.0 DEX0455_022.nt.1 20299.01 17.6 18.8 23.1 25.0 0.0 0.0DEX0455_022.nt.1 20299.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.120311.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.1 20311.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_022.nt.1 20317.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_022.nt.1 20317.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.29920.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_022.nt.2 9920.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_022.nt.2 20299.01 17.6 18.8 23.1 25.0 0.0 0.0DEX0455_022.nt.2 20299.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.220311.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.2 20311.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_022.nt.2 20317.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_022.nt.2 20317.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.39920.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_022.nt.3 9920.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_022.nt.3 20311.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_022.nt.3 20311.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.320317.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_022.nt.3 20317.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_023.nt.1 16187.01 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_023.nt.1 16187.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_023.nt.116374.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_023.nt.1 16374.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_023.nt.1 16378.01 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_023.nt.1 16378.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_024.nt.112149.01 52.9 52.9 46.2 46.2 75.0 75.0 DEX0455_024.nt.1 12149.02 47.147.1 38.5 38.5 75.0 75.0 DEX0455_024.nt.1 21487.01 5.9 6.7 7.7 8.3 0.00.0 DEX0455_024.nt.1 21487.02 17.6 18.8 15.4 16.7 25.0 25.0DEX0455_024.nt.1 21507.01 29.4 29.4 23.1 23.1 50.0 50.0 DEX0455_024.nt.121507.02 29.4 31.2 23.1 25.0 50.0 50.0 DEX0455_024.nt.1 21547.01 47.147.1 46.2 46.2 50.0 50.0 DEX0455_024.nt.1 21547.02 41.2 41.2 38.5 38.550.0 50.0 DEX0455_024.nt.2 12149.01 52.9 52.9 46.2 46.2 75.0 75.0DEX0455_024.nt.2 12149.02 47.1 47.1 38.5 38.5 75.0 75.0 DEX0455_024.nt.221507.01 29.4 29.4 23.1 23.1 50.0 50.0 DEX0455_024.nt.2 21507.02 29.431.2 23.1 25.0 50.0 50.0 DEX0455_024.nt.2 21547.01 47.1 47.1 46.2 46.250.0 50.0 DEX0455_024.nt.2 21547.02 41.2 41.2 38.5 38.5 50.0 50.0DEX0455_025.nt.1 12167.01 17.6 18.8 23.1 23.1 0.0 0.0 DEX0455_025.nt.112167.02 11.8 11.8 15.4 15.4 0.0 0.0 DEX0455_025.nt.1 16956.01 5.9 5.97.7 7.7 0.0 0.0 DEX0455_025.nt.1 16956.02 5.9 5.9 7.7 7.7 0.0 0.0DEX0455_025.nt.1 16958.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.116958.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.1 16964.01 5.9 5.9 7.77.7 0.0 0.0 DEX0455_025.nt.1 16964.02 5.9 5.9 7.7 7.7 0.0 0.0DEX0455_025.nt.1 19010.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.119010.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.2 12167.01 17.6 18.823.1 23.1 0.0 0.0 DEX0455_025.nt.2 12167.02 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_025.nt.2 16956.01 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.216956.02 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.2 16958.01 0.0 0.0 0.00.0 0.0 0.0 DEX0455_025.nt.2 16958.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_025.nt.2 16964.01 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.216964.02 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.2 19010.01 0.0 0.0 0.00.0 0.0 0.0 DEX0455_025.nt.2 19010.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_025.nt.3 12167.01 17.6 18.8 23.1 23.1 0.0 0.0 DEX0455_025.nt.312167.02 11.8 11.8 15.4 15.4 0.0 0.0 DEX0455_025.nt.3 16958.01 0.0 0.00.0 0.0 0.0 0.0 DEX0455_025.nt.3 16958.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_025.nt.3 19010.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.319010.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_025.nt.4 12167.01 17.6 18.823.1 23.1 0.0 0.0 DEX0455_025.nt.4 12167.02 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_025.nt.4 16956.01 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.416956.02 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.4 16958.01 0.0 0.0 0.00.0 0.0 0.0 DEX0455_025.nt.4 16958.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_025.nt.4 16964.01 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.416964.02 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_025.nt.4 19010.01 0.0 0.0 0.00.0 0.0 0.0 DEX0455_025.nt.4 19010.02 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_027.nt.1 21549.01 29.4 31.2 23.1 25.0 50.0 50.0 DEX0455_027.nt.121549.02 29.4 31.2 23.1 25.0 50.0 50.0 DEX0455_029.nt.1 17430.01 23.523.5 30.8 30.8 0.0 0.0 DEX0455_029.nt.1 17430.02 17.6 17.6 23.1 23.1 0.00.0 DEX0455_029.nt.1 17448.01 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_029.nt.1 17448.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_029.nt.122113.01 11.8 25.0 15.4 28.6 0.0 0.0 DEX0455_029.nt.1 22113.02 11.8 20.015.4 25.0 0.0 0.0 DEX0455_029.nt.1 23386.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_029.nt.1 23386.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_029.nt.123400.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_029.nt.1 23400.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_029.nt.2 17424.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_029.nt.2 17424.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_029.nt.217430.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_029.nt.2 17430.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_029.nt.2 17448.01 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_029.nt.2 17448.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_029.nt.222113.01 11.8 25.0 15.4 28.6 0.0 0.0 DEX0455_029.nt.2 22113.02 11.8 20.015.4 25.0 0.0 0.0 DEX0455_029.nt.2 23386.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_029.nt.2 23386.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_029.nt.223400.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_029.nt.2 23400.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_030.nt.1 11613.01 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_030.nt.1 11613.02 11.8 13.3 15.4 16.7 0.0 0.0 DEX0455_030.nt.117204.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_030.nt.1 17204.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_030.nt.1 17262.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_030.nt.1 17262.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_030.nt.117278.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_030.nt.1 17278.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_030.nt.2 11613.01 11.8 11.8 15.4 15.4 0.0 0.0DEX0455_030.nt.2 11613.02 11.8 13.3 15.4 16.7 0.0 0.0 DEX0455_030.nt.217204.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_030.nt.2 17204.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_030.nt.2 17262.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_030.nt.2 17262.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_030.nt.217274.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_030.nt.2 17274.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_030.nt.2 17278.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_030.nt.2 17278.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_031.nt.120773.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_031.nt.1 20773.02 23.5 25.030.8 33.3 0.0 0.0 DEX0455_031.nt.2 20773.01 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_031.nt.2 20773.02 23.5 25.0 30.8 33.3 0.0 0.0 DEX0455_031.nt.320773.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_031.nt.3 20773.02 23.5 25.030.8 33.3 0.0 0.0 DEX0455_032.nt.1 11585.01 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_032.nt.1 11585.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_032.nt.118556.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_032.nt.1 18556.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_034.nt.1 10722.01 82.4 82.4 84.6 84.6 75.0 75.0DEX0455_034.nt.1 10722.02 76.5 81.2 84.6 84.6 50.0 66.7 DEX0455_034.nt.121401.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_034.nt.1 21401.02 5.9 6.7 7.78.3 0.0 0.0 DEX0455_034.nt.1 21421.01 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_034.nt.1 21421.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_035.nt.1103385.01 58.8 58.8 76.9 76.9 0.0 0.0 DEX0455_035.nt.1 103385.02 58.858.8 76.9 76.9 0.0 0.0 DEX0455_035.nt.2 103385.01 58.8 58.8 76.9 76.90.0 0.0 DEX0455_035.nt.2 103385.02 58.8 58.8 76.9 76.9 0.0 0.0DEX0455_035.nt.3 103385.01 58.8 58.8 76.9 76.9 0.0 0.0 DEX0455_035.nt.3103385.02 58.8 58.8 76.9 76.9 0.0 0.0 DEX0455_036.nt.1 92327.01 52.956.2 61.5 66.7 25.0 25.0 DEX0455_036.nt.1 92327.02 52.9 52.9 61.5 61.525.0 25.0 DEX0455_036.nt.2 92327.01 52.9 56.2 61.5 66.7 25.0 25.0DEX0455_036.nt.2 92327.02 52.9 52.9 61.5 61.5 25.0 25.0 DEX0455_036.nt.392327.01 52.9 56.2 61.5 66.7 25.0 25.0 DEX0455_036.nt.3 92327.02 52.952.9 61.5 61.5 25.0 25.0 DEX0455_036.nt.4 92327.01 52.9 56.2 61.5 66.725.0 25.0 DEX0455_036.nt.4 92327.02 52.9 52.9 61.5 61.5 25.0 25.0DEX0455_037.nt.1 11575.01 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.111575.02 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.1 17486.01 47.147.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.1 17486.02 47.1 47.1 46.2 46.250.0 50.0 DEX0455_037.nt.1 17490.01 52.9 52.9 53.8 53.8 50.0 50.0DEX0455_037.nt.1 17490.02 58.8 58.8 53.8 53.8 75.0 75.0 DEX0455_037.nt.211575.01 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.2 11575.02 52.952.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.2 17486.01 47.1 47.1 46.2 46.250.0 50.0 DEX0455_037.nt.2 17486.02 47.1 47.1 46.2 46.2 50.0 50.0DEX0455_037.nt.2 17490.01 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.217490.02 58.8 58.8 53.8 53.8 75.0 75.0 DEX0455_037.nt.3 11575.01 52.952.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.3 11575.02 52.9 52.9 53.8 53.850.0 50.0 DEX0455_037.nt.3 17486.01 47.1 47.1 46.2 46.2 50.0 50.0DEX0455_037.nt.3 17486.02 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.317490.01 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.3 17490.02 58.858.8 53.8 53.8 75.0 75.0 DEX0455_037.nt.4 11575.01 52.9 52.9 53.8 53.850.0 50.0 DEX0455_037.nt.4 11575.02 52.9 52.9 53.8 53.8 50.0 50.0DEX0455_037.nt.4 17486.01 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.417486.02 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.4 17490.01 52.952.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.4 17490.02 58.8 58.8 53.8 53.875.0 75.0 DEX0455_037.nt.5 11575.01 52.9 52.9 53.8 53.8 50.0 50.0DEX0455_037.nt.5 11575.02 52.9 52.9 53.8 53.8 50.0 50.0 DEX0455_037.nt.517486.01 47.1 47.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.5 17486.02 47.147.1 46.2 46.2 50.0 50.0 DEX0455_037.nt.5 17490.01 52.9 52.9 53.8 53.850.0 50.0 DEX0455_037.nt.5 17490.02 58.8 58.8 53.8 53.8 75.0 75.0DEX0455_039.nt.1 21505.01 94.1 94.1 92.3 92.3 100.0 100.0DEX0455_039.nt.1 21505.02 94.1 94.1 92.3 92.3 100.0 100.0DEX0455_039.nt.2 11527.01 88.2 88.2 84.6 84.6 100.0 100.0DEX0455_039.nt.2 11527.02 88.2 88.2 84.6 84.6 100.0 100.0DEX0455_040.nt.1 21489.01 11.8 11.8 15.4 15.4 0.0 0.0 DEX0455_040.nt.121489.02 17.6 18.8 23.1 23.1 0.0 0.0 DEX0455_040.nt.1 21501.01 47.1 50.061.5 61.5 0.0 0.0 DEX0455_040.nt.1 21501.02 41.2 41.2 53.8 53.8 0.0 0.0DEX0455_040.nt.1 21511.01 47.1 47.1 61.5 61.5 0.0 0.0 DEX0455_040.nt.121511.02 47.1 47.1 53.8 53.8 25.0 25.0 DEX0455_040.nt.2 21489.01 11.811.8 15.4 15.4 0.0 0.0 DEX0455_040.nt.2 21489.02 17.6 18.8 23.1 23.1 0.00.0 DEX0455_040.nt.2 21501.01 47.1 50.0 61.5 61.5 0.0 0.0DEX0455_040.nt.2 21501.02 41.2 41.2 53.8 53.8 0.0 0.0 DEX0455_040.nt.221511.01 47.1 47.1 61.5 61.5 0.0 0.0 DEX0455_040.nt.2 21511.02 47.1 47.153.8 53.8 25.0 25.0 DEX0455_041.nt.1 12155.01 23.5 23.5 30.8 30.8 0.00.0 DEX0455_041.nt.1 12155.02 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_041.nt.1 16980.01 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_041.nt.116980.02 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_041.nt.2 12155.01 23.5 23.530.8 30.8 0.0 0.0 DEX0455_041.nt.2 12155.02 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_042.nt.1 18214.01 94.1 94.1 92.3 92.3 100.0 100.0DEX0455_042.nt.1 18214.02 88.2 93.8 84.6 91.7 100.0 100.0DEX0455_043.nt.1 14656.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_043.nt.114656.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_043.nt.3 14656.01 17.6 17.623.1 23.1 0.0 0.0 DEX0455_043.nt.3 14656.02 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_045.nt.1 36013.01 23.5 23.5 7.7 7.7 75.0 75.0 DEX0455_045.nt.136013.02 11.8 11.8 0.0 0.0 50.0 50.0 DEX0455_046.nt.1 17314.01 23.5 26.715.4 16.7 50.0 66.7 DEX0455_046.nt.1 17314.02 23.5 26.7 15.4 16.7 50.066.7 DEX0455_049.nt.1 11511.01 94.1 100.0 92.3 100.0 100.0 100.0DEX0455_049.nt.1 11511.02 88.2 100.0 84.6 100.0 100.0 100.0DEX0455_049.nt.2 11511.01 94.1 100.0 92.3 100.0 100.0 100.0DEX0455_049.nt.2 11511.02 88.2 100.0 84.6 100.0 100.0 100.0DEX0455_049.nt.4 11511.01 94.1 100.0 92.3 100.0 100.0 100.0DEX0455_049.nt.4 11511.02 88.2 100.0 84.6 100.0 100.0 100.0DEX0455_049.nt.5 11511.01 94.1 100.0 92.3 100.0 100.0 100.0DEX0455_049.nt.5 11511.02 88.2 100.0 84.6 100.0 100.0 100.0DEX0455_050.nt.1 23378.01 11.8 18.2 15.4 20.0 0.0 0.0 DEX0455_050.nt.123378.02 17.6 23.1 7.7 9.1 50.0 100.0 DEX0455_052.nt.1 91971.01 94.194.1 92.3 92.3 100.0 100.0 DEX0455_052.nt.1 91971.02 94.1 94.1 92.3 92.3100.0 100.0 DEX0455_055.nt.1 11273.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_055.nt.1 11273.02 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_055.nt.120541.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_055.nt.1 20541.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_055.nt.2 11273.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_055.nt.2 11273.02 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_055.nt.220541.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_055.nt.2 20541.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_055.nt.3 11273.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_055.nt.3 11273.02 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_055.nt.320541.01 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_055.nt.3 20541.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_056.nt.1 18520.01 23.5 23.5 30.8 30.8 0.0 0.0DEX0455_056.nt.1 18520.02 17.6 17.6 23.1 23.1 0.0 0.0 DEX0455_056.nt.122734.01 5.9 5.9 7.7 7.7 0.0 0.0 DEX0455_056.nt.1 22734.02 23.5 23.530.8 30.8 0.0 0.0 DEX0455_056.nt.1 23444.01 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 23444.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_056.nt.218520.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_056.nt.2 18520.02 17.6 17.623.1 23.1 0.0 0.0 DEX0455_056.nt.2 22734.01 5.9 5.9 7.7 7.7 0.0 0.0DEX0455_056.nt.2 22734.02 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_056.nt.223444.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_056.nt.2 23444.02 0.0 0.0 0.00.0 0.0 0.0 DEX0455_057.nt.1 24524.01 70.6 70.6 69.2 69.2 75.0 75.0DEX0455_057.nt.1 24524.02 70.6 70.6 69.2 69.2 75.0 75.0 DEX0455_057.nt.224524.01 70.6 70.6 69.2 69.2 75.0 75.0 DEX0455_057.nt.2 24524.02 70.670.6 69.2 69.2 75.0 75.0 DEX0455_058.nt.1 14656.01 17.6 17.6 23.1 23.10.0 0.0 DEX0455_058.nt.1 14656.02 17.6 17.6 23.1 23.1 0.0 0.0DEX0455_059.nt.1 11469.01 47.1 47.1 61.5 61.5 0.0 0.0 DEX0455_059.nt.111469.02 52.9 52.9 61.5 61.5 25.0 25.0 DEX0455_059.nt.1 17370.01 5.925.0 7.7 25.0 0.0 0.0 DEX0455_059.nt.1 17370.02 5.9 25.0 7.7 25.0 0.00.0 DEX0455_059.nt.1 17372.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_059.nt.117372.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_059.nt.2 11469.01 47.1 47.161.5 61.5 0.0 0.0 DEX0455_059.nt.2 11469.02 52.9 52.9 61.5 61.5 25.025.0 DEX0455_059.nt.2 17372.01 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_059.nt.217372.02 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_060.nt.1 10372.01 35.3 35.346.2 46.2 0.0 0.0 DEX0455_060.nt.1 10372.02 35.3 35.3 46.2 46.2 0.0 0.0DEX0455_060.nt.1 18582.01 23.5 23.5 30.8 30.8 0.0 0.0 DEX0455_060.nt.118582.02 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_061.nt.1 96523.01 23.5 23.515.4 15.4 50.0 50.0 DEX0455_061.nt.1 96523.02 17.6 17.6 7.7 7.7 50.050.0 DEX0455_061.nt.1 103529.01 23.5 25.0 15.4 16.7 50.0 50.0DEX0455_061.nt.1 103529.02 23.5 23.5 15.4 15.4 50.0 50.0DEX0455_061.nt.2 96523.01 23.5 23.5 15.4 15.4 50.0 50.0 DEX0455_061.nt.296523.02 17.6 17.6 7.7 7.7 50.0 50.0 DEX0455_061.nt.2 103529.01 23.525.0 15.4 16.7 50.0 50.0 DEX0455_061.nt.2 103529.02 23.5 23.5 15.4 15.450.0 50.0 DEX0455_061.nt.3 96523.01 23.5 23.5 15.4 15.4 50.0 50.0DEX0455_061.nt.3 96523.02 17.6 17.6 7.7 7.7 50.0 50.0 DEX0455_061.nt.3103529.01 23.5 25.0 15.4 16.7 50.0 50.0 DEX0455_061.nt.3 103529.02 23.523.5 15.4 15.4 50.0 50.0 DEX0455_061.nt.4 96523.01 23.5 23.5 15.4 15.450.0 50.0 DEX0455_061.nt.4 96523.02 17.6 17.6 7.7 7.7 50.0 50.0DEX0455_061.nt.4 103529.01 23.5 25.0 15.4 16.7 50.0 50.0DEX0455_061.nt.4 103529.02 23.5 23.5 15.4 15.4 50.0 50.0DEX0455_061.nt.5 96523.01 23.5 23.5 15.4 15.4 50.0 50.0 DEX0455_061.nt.596523.02 17.6 17.6 7.7 7.7 50.0 50.0 DEX0455_061.nt.5 103529.01 23.525.0 15.4 16.7 50.0 50.0 DEX0455_061.nt.5 103529.02 23.5 23.5 15.4 15.450.0 50.0 DEX0455_062.nt.1 17464.01 29.4 29.4 38.5 38.5 0.0 0.0DEX0455_062.nt.1 17464.02 29.4 29.4 38.5 38.5 0.0 0.0 DEX0455_062.nt.118094.01 52.9 52.9 69.2 69.2 0.0 0.0 DEX0455_062.nt.1 18094.02 52.9 52.969.2 69.2 0.0 0.0

TABLE 2 Ovr Ovr Ovr Ovr Multi- Ovr Multi- Ovr Multi- Multi- CancerMulti- Cancer Multi- Cancer Cancer ALL Cancer INV Cancer LMP Oligo ALL %up % valid INV % up % valid LMP % up % valid DEX ID Name n = 19 up n =19 n = 14 up n = 14 n = 5 up n = 5 DEX0455_002.nt.1 79699.1 10.5 10.514.3 14.3 0.0 0.0 DEX0455_002.nt.1 79700.0 10.5 10.5 14.3 14.3 0.0 0.0DEX0455_002.nt.1 79700.1 26.3 26.3 21.4 21.4 40.0 40.0 DEX0455_004.nt.196339.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 96339.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.1 96340.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 96340.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105991.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105991.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.1 105992.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105992.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105996.0 21.1 21.1 28.6 28.6 0.0 0.0 DEX0455_004.nt.1 105996.1 21.1 21.128.6 28.6 0.0 0.0 DEX0455_004.nt.2 96339.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 96339.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.296340.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 96340.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.2 105991.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 105991.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2105992.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105992.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 105996.0 21.1 21.1 28.6 28.6 0.0 0.0DEX0455_004.nt.2 105996.1 21.1 21.1 28.6 28.6 0.0 0.0 DEX0455_011.nt.135317.0 31.6 42.9 14.3 20.0 80.0 100.0 DEX0455_011.nt.1 35317.1 31.635.3 14.3 15.4 80.0 100.0 DEX0455_012.nt.1 34334.0 89.5 89.5 85.7 85.7100.0 100.0 DEX0455_012.nt.1 34334.1 84.2 88.9 85.7 85.7 80.0 100.0DEX0455_012.nt.1 34335.0 94.7 100.0 92.9 100.0 100.0 100.0DEX0455_012.nt.1 34335.1 89.5 100.0 92.9 100.0 80.0 100.0DEX0455_012.nt.2 34334.0 89.5 89.5 85.7 85.7 100.0 100.0DEX0455_012.nt.2 34334.1 84.2 88.9 85.7 85.7 80.0 100.0 DEX0455_012.nt.234335.0 94.7 100.0 92.9 100.0 100.0 100.0 DEX0455_012.nt.2 34335.1 89.5100.0 92.9 100.0 80.0 100.0 DEX0455_017.nt.1 36482.0 31.6 42.9 28.6 40.040.0 50.0 DEX0455_017.nt.1 36482.1 31.6 50.0 28.6 44.4 40.0 66.7DEX0455_033.nt.1 2023.0 21.1 23.5 28.6 30.8 0.0 0.0 DEX0455_033.nt.15327.0 15.8 16.7 21.4 21.4 0.0 0.0 DEX0455_033.nt.1 5328.0 10.5 11.114.3 14.3 0.0 0.0 DEX0455_035.nt.1 78519.0 42.1 47.1 57.1 57.1 0.0 0.0DEX0455_035.nt.1 78519.1 47.4 52.9 64.3 69.2 0.0 0.0 DEX0455_035.nt.178520.0 36.8 38.9 50.0 50.0 0.0 0.0 DEX0455_035.nt.1 78520.1 42.1 44.457.1 57.1 0.0 0.0 DEX0455_035.nt.2 78519.0 42.1 47.1 57.1 57.1 0.0 0.0DEX0455_035.nt.2 78519.1 47.4 52.9 64.3 69.2 0.0 0.0 DEX0455_035.nt.278520.0 36.8 38.9 50.0 50.0 0.0 0.0 DEX0455_035.nt.2 78520.1 42.1 44.457.1 57.1 0.0 0.0 DEX0455_035.nt.3 78519.0 42.1 47.1 57.1 57.1 0.0 0.0DEX0455_035.nt.3 78519.1 47.4 52.9 64.3 69.2 0.0 0.0 DEX0455_035.nt.378520.0 36.8 38.9 50.0 50.0 0.0 0.0 DEX0455_035.nt.3 78520.1 42.1 44.457.1 57.1 0.0 0.0 DEX0455_038.nt.1 23542.0 5.3 5.6 7.1 7.7 0.0 0.0DEX0455_038.nt.1 23542.1 10.5 10.5 14.3 14.3 0.0 0.0 DEX0455_038.nt.123543.0 15.8 16.7 14.3 15.4 20.0 20.0 DEX0455_038.nt.1 23543.1 21.1 21.121.4 21.4 20.0 20.0 DEX0455_038.nt.2 23542.0 5.3 5.6 7.1 7.7 0.0 0.0DEX0455_038.nt.2 23542.1 10.5 10.5 14.3 14.3 0.0 0.0 DEX0455_038.nt.223543.0 15.8 16.7 14.3 15.4 20.0 20.0 DEX0455_038.nt.2 23543.1 21.1 21.121.4 21.4 20.0 20.0 DEX0455_038.nt.3 23542.0 5.3 5.6 7.1 7.7 0.0 0.0DEX0455_038.nt.3 23542.1 10.5 10.5 14.3 14.3 0.0 0.0 DEX0455_038.nt.323543.0 15.8 16.7 14.3 15.4 20.0 20.0 DEX0455_038.nt.3 23543.1 21.1 21.121.4 21.4 20.0 20.0 DEX0455_047.nt.1 96212.0 10.5 11.8 14.3 15.4 0.0 0.0DEX0455_047.nt.1 96212.1 5.3 5.9 7.1 7.7 0.0 0.0 DEX0455_047.nt.1105764.0 10.5 12.5 14.3 15.4 0.0 0.0 DEX0455_047.nt.1 105764.1 15.8 16.714.3 15.4 20.0 20.0 DEX0455_047.nt.1 105767.0 15.8 15.8 14.3 14.3 20.020.0 DEX0455_047.nt.1 105767.1 15.8 15.8 14.3 14.3 20.0 20.0DEX0455_047.nt.1 105768.0 15.8 15.8 14.3 14.3 20.0 20.0 DEX0455_047.nt.1105768.1 21.1 22.2 21.4 23.1 20.0 20.0 DEX0455_047.nt.2 96212.0 10.511.8 14.3 15.4 0.0 0.0 DEX0455_047.nt.2 96212.1 5.3 5.9 7.1 7.7 0.0 0.0DEX0455_047.nt.2 105764.0 10.5 12.5 14.3 15.4 0.0 0.0 DEX0455_047.nt.2105764.1 15.8 16.7 14.3 15.4 20.0 20.0 DEX0455_047.nt.2 105767.0 15.815.8 14.3 14.3 20.0 20.0 DEX0455_047.nt.2 105767.1 15.8 15.8 14.3 14.320.0 20.0 DEX0455_047.nt.2 105768.0 15.8 15.8 14.3 14.3 20.0 20.0DEX0455_047.nt.2 105768.1 21.1 22.2 21.4 23.1 20.0 20.0 DEX0455_048.nt.11168.0 10.5 10.5 14.3 14.3 0.0 0.0 DEX0455_048.nt.2 1175.0 0.0 0.0 0.00.0 0.0 0.0 DEX0455_050.nt.1 23378.0 5.3 5.3 7.1 7.1 0.0 0.0DEX0455_050.nt.1 23378.1 5.3 5.3 7.1 7.1 0.0 0.0 DEX0455_050.nt.123379.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23379.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42007.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.142007.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42008.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42008.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42008.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.178508.0 21.1 21.1 21.4 21.4 20.0 20.0 DEX0455_061.nt.1 78508.1 21.1 21.121.4 21.4 20.0 20.0 DEX0455_061.nt.2 78508.0 21.1 21.1 21.4 21.4 20.020.0 DEX0455_061.nt.2 78508.1 21.1 21.1 21.4 21.4 20.0 20.0DEX0455_061.nt.3 78508.0 21.1 21.1 21.4 21.4 20.0 20.0 DEX0455_061.nt.378508.1 21.1 21.1 21.4 21.4 20.0 20.0 DEX0455_061.nt.4 78508.0 21.1 21.121.4 21.4 20.0 20.0 DEX0455_061.nt.4 78508.1 21.1 21.1 21.4 21.4 20.020.0 DEX0455_061.nt.5 78508.0 21.1 21.1 21.4 21.4 20.0 20.0DEX0455_061.nt.5 78508.1 21.1 21.1 21.4 21.4 20.0 20.0

Breast Cancer Chips

For breast cancer two different chip designs were evaluated withoverlapping sets of a total of 36 samples, comparing the expressionpatterns of breast cancer derived polyA+RNA to polyA+RNA isolated from apool of 10 normal breast tissues. For the Breast Array Chip, all 36samples (9 stage I cancers, 23 stage II cancers, 4 stage III cancers)were analyzed. These samples also represented 10 Grade1/2 and 26 Grade 3cancers. The histopathologic grades for cancer are classified asfollows: GX, cannot be assessed; G1, well differentiated; G2, moderatelydifferentiated; G3, poorly differentiated; and G4, undifferentiated.AJCC Cancer Staging Handbook, pp. 9, (5th Ed, 1998). Samples werefurther grouped based on the expression patterns of the known breastcancer associated genes Hex2 and ERα (10 HER2 up, 26 HER2 not up, 20 ERup and 16 ER not up) and for the Multi-Cancer Array Chip, a subset of 20of these samples (9 stage I cancers, 8 stage II cancers, 3 stage IIIcancers) were assessed.

The results for the statistically significant up-regulated genes on theBreast Array Chip are shown in Tables 3 and 4. The results for thestatistically significant up-regulated genes on the Multi-Cancer ArrayChip are shown in Table 5. The first two columns of each table containinformation about the sequence itself (Seq ID, Oligo Name), the nextcolumns show the results obtained for all (“ALL”) breast cancer samples,cancers corresponding to stageI (“ST1”), stages II and III (“ST2,3”),grades 1 and 2 (“GR1,2”), grade 3 (“GR3”), cancers exhibitingup-regulation of Her2 (“HER2up”) or ERα (“ERup”) or those not exhibitingup-regulation of Her2 (“NOT HER2up”) or ERα (“NOT ERup”). ‘% up’indicates the percentage of all experiments in which up-regulation of atleast 2-fold was observed (n=736 for Colon Array Chip, n=20 for theMulti-Cancer Array Chip), ‘% valid up’ indicates the percentage ofexperiments with valid expression values in which up-regulation of atleast 2-fold was observed. TABLE 3 Mam Mam Mam Mam Mam Mam ALL % Mam ST1% Mam ST2,3 % Mam GR1,2 % Mam GR3 % ALL valid ST1 valid ST2,3 validGR1,2 valid GR3 valid Oligo % up up % up up % up up % up up % up up DEXID Name n = 36 n = 36 n = 9 n = 9 n = 27 n = 27 n = 10 n = 10 n = 26 n =26 DEX0455_010.nt.1 32151.0 22.2 22.2 44.4 44.4 14.8 14.8 10.0 10.0 26.926.9 DEX0455_017.nt.1 28221.0 2.8 3.1 0.0 0.0 3.7 4.3 0.0 0.0 3.8 4.5DEX0455_022.nt.1 23280.0 11.1 11.8 11.1 11.1 11.1 12.0 10.0 10.0 11.512.5 DEX0455_035.nt.3 21143.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_035.nt.3 21144.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_041.nt.1 16998.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_046.nt.1 19072.0 11.1 11.4 0.0 0.0 14.8 15.4 20.0 20.0 7.7 8.0DEX0455_050.nt.1 22136.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 5.6 5.7 0.0 0.0 7.4 7.7 0.0 0.0 7.7 8.0DEX0455_050.nt.1 23379.2 5.6 5.7 0.0 0.0 7.4 7.7 0.0 0.0 7.7 8.0DEX0455_050.nt.1 29736.0 2.8 2.8 0.0 0.0 3.7 3.7 0.0 0.0 3.8 3.8DEX0455_054.nt.1 19799.0 8.3 8.3 0.0 0.0 11.1 11.1 0.0 0.0 11.5 11.5DEX0455_055.nt.1 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.1 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.2 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.2 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.3 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.3 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

TABLE 4 Mam Mam Mam Mam NOT Mam Mam NOT Mam HER2up NOT HER2up Mam ERupNOT ERup HER2up % valid HER2up % valid ERup % valid ERup % valid Oligo %up up % up up % up up % up up DEX ID Name n = 10 n = 10 n = 26 n = 26 n= 20 n = 20 n = 16 n = 16 DEX0455_010.nt.1 32151.0 20.0 20.0 23.1 23.110.0 10.0 37.5 37.5 DEX0455_017.nt.1 28221.0 10.0 11.1 0.0 0.0 0.0 0.06.2 8.3 DEX0455_022.nt.1 23280.0 20.0 20.0 7.7 8.3 10.0 11.1 12.5 12.5DEX0455_035.nt.3 21143.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_035.nt.3 21144.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_041.nt.1 16998.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_046.nt.1 19072.0 20.0 20.0 7.7 8.0 15.0 15.0 6.2 6.7DEX0455_050.nt.1 22136.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 0.0 0.0 7.7 8.0 0.0 0.0 12.5 13.3DEX0455_050.nt.1 23379.2 0.0 0.0 7.7 8.0 0.0 0.0 12.5 13.3DEX0455_050.nt.1 29736.0 0.0 0.0 3.8 3.8 0.0 0.0 6.2 6.2DEX0455_054.nt.1 19799.0 10.0 10.0 7.7 7.7 10.0 10.0 6.2 6.2DEX0455_055.nt.1 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.1 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.2 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.2 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.3 12731.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_055.nt.3 12732.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

TABLE 5 Mam Mam Mam Mam Mam Multi- Mam Multi- Multi- Multi- Multi-Cancer Multi- Cancer Cancer Cancer Cancer ALL Cancer ST1 ST2,3 ST2,3Oligo ALL % up % valid ST1 % up % valid % up % valid DEX ID Name n = 20up n = 20 n = 9 up n = 9 n = 11 up n = 11 DEX0455_002.nt.1 79699.1 20.020.0 44.4 44.4 0.0 0.0 DEX0455_002.nt.1 79700.0 10.0 10.0 22.2 22.2 0.00.0 DEX0455_002.nt.1 79700.1 15.0 15.0 33.3 33.3 0.0 0.0DEX0455_004.nt.1 96339.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.196339.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 96340.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.1 96340.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105991.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105991.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105992.0 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.1 105992.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105996.0 15.0 15.0 11.1 11.1 18.2 18.2 DEX0455_004.nt.1105996.1 15.0 15.0 11.1 11.1 18.2 18.2 DEX0455_004.nt.2 96339.0 0.0 0.00.0 0.0 0.0 0.0 DEX0455_004.nt.2 96339.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 96340.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.296340.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105991.0 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 105991.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 105992.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2105992.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105996.0 15.0 15.011.1 11.1 18.2 18.2 DEX0455_004.nt.2 105996.1 15.0 15.0 11.1 11.1 18.218.2 DEX0455_011.nt.1 35317.0 5.0 7.1 11.1 20.0 0.0 0.0 DEX0455_011.nt.135317.1 5.0 7.1 11.1 20.0 0.0 0.0 DEX0455_012.nt.1 34334.0 5.0 5.0 0.00.0 9.1 9.1 DEX0455_012.nt.1 34334.1 5.0 5.0 0.0 0.0 9.1 9.1DEX0455_012.nt.1 34335.0 5.0 5.0 0.0 0.0 9.1 9.1 DEX0455_012.nt.134335.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.2 34334.0 5.0 5.0 0.0 0.09.1 9.1 DEX0455_012.nt.2 34334.1 5.0 5.0 0.0 0.0 9.1 9.1DEX0455_012.nt.2 34335.0 5.0 5.0 0.0 0.0 9.1 9.1 DEX0455_012.nt.234335.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_017.nt.1 36482.0 10.0 10.0 11.111.1 9.1 9.1 DEX0455_017.nt.1 36482.1 10.0 10.0 11.1 11.1 9.1 9.1DEX0455_033.nt.1 2023.0 10.0 10.0 0.0 0.0 18.2 18.2 DEX0455_033.nt.15327.0 10.0 10.0 0.0 0.0 18.2 18.2 DEX0455_033.nt.1 5328.0 10.0 10.0 0.00.0 18.2 18.2 DEX0455_035.nt.1 78519.0 50.0 50.0 66.7 66.7 36.4 36.4DEX0455_035.nt.1 78519.1 40.0 40.0 66.7 66.7 18.2 18.2 DEX0455_035.nt.178520.0 20.0 20.0 33.3 33.3 9.1 9.1 DEX0455_035.nt.1 78520.1 20.0 20.033.3 33.3 9.1 9.1 DEX0455_035.nt.2 78519.0 50.0 50.0 66.7 66.7 36.4 36.4DEX0455_035.nt.2 78519.1 40.0 40.0 66.7 66.7 18.2 18.2 DEX0455_035.nt.278520.0 20.0 20.0 33.3 33.3 9.1 9.1 DEX0455_035.nt.2 78520.1 20.0 20.033.3 33.3 9.1 9.1 DEX0455_035.nt.3 78519.0 50.0 50.0 66.7 66.7 36.4 36.4DEX0455_035.nt.3 78519.1 40.0 40.0 66.7 66.7 18.2 18.2 DEX0455_035.nt.378520.0 20.0 20.0 33.3 33.3 9.1 9.1 DEX0455_035.nt.3 78520.1 20.0 20.033.3 33.3 9.1 9.1 DEX0455_038.nt.1 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.1 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.123543.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 23543.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_038.nt.2 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.2 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.223543.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23543.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_038.nt.3 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.3 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.323543.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.3 23543.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_047.nt.1 96212.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.1 96212.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1105764.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105764.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.1 105767.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.1 105767.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1105768.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105768.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.2 96212.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.2 96212.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2105764.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105764.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.2 105767.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.2 105767.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2105768.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105768.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_048.nt.1 1168.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_048.nt.2 1175.0 5.0 5.0 0.0 0.0 9.1 9.1 DEX0455_050.nt.1 23378.00.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.123379.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42007.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42007.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.142008.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42008.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42008.2 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.1 78508.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.178508.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.2 78508.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_061.nt.2 78508.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.3 78508.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.378508.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.4 78508.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_061.nt.4 78508.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.5 78508.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.578508.1 0.0 0.0 0.0 0.0 0.0 0.0

Colon Cancer Chips

For colon cancer two different chip designs were evaluated withoverlapping sets of a total of 38 samples, comparing the expressionpatterns of colon cancer derived polyA+RNA to polyA+RNA isolated from apool of 7 normal colon tissues. For the Colon Array Chip all 38 samples(23 Ascending colon carcinomas and 15 Rectosigmoidal carcinomasincluding: 5 stage I cancers, 15 stage II cancers, 15 stage III and 2stage IV cancers, as well as 28 Grade1/2 and 10 Grade 3 cancers) wereanalyzed. The histopathologic grades for cancer are classified asfollows: GX, cannot be assessed; G1, well differentiated; G2, Moderatelydifferentiated; G3, poorly differentiated; and G4, undifferentiated.AJCC Cancer Staging Handbook, 5^(th) Edition, 1998, page 9. For theColon Array Chip analysis, samples were further divided into groupsbased on the expression pattern of the known colon cancer associatedgene Thymidilate Synthase (TS) (13 TS up 25 TS not up). The associationof TS with advanced colorectal cancer is well documented. Paradiso etal., Br J Cancer 82(3):560-7 (2000); Etienne et al., J. Clin Oncol.20(12):283243 (2002); Aschele et al. Clin Cancer Res. 6(12):4797-802(2000). For the Multi-Cancer Array Chip a subset of 27 of these samples(14 Ascending colon carcinomas and 13 Rectosigmoidal carcinomasincluding: 3 stage I cancers, 9 stage II cancers, 13 stage III and 2stage IV cancers) were assessed.

The results for the statistically significant up-regulated genes on theColon Array Chip are shown in Tables 6 and 7. The results for thestatistically significant up-regulated genes on the Multi-Cancer ArrayChip are shown in Table 8.

The first two columns of each table contain information about thesequence itself (Seq ID, Oligo Name), the next columns show the resultsobtained for all (“ALL”) the colon samples, ascending colon carcinomas(“ASC”), Rectosigmoidal carcinomas (“RS”), cancers corresponding tostages I and II (“ST1,2”), stages III and IV (“ST3,4”), grades 1 and 2(“GR1,2”), grade 3 (“GR3”), cancers exhibiting up-regulation of the TSgene (“TSup”) or those not exhibiting up-regulation of the TS gene (“NOTTSup”). ‘% up’ indicates the percentage of all experiments in whichupregulation of at least 2-fold was observed n=38 for the Colon ArrayChip (n=27 for the Multi-Cancer Array Chip), ‘% valid up’ indicates thepercentage of experiments with valid expression values in whichup-regulation of at least 2-fold was observed. TABLE 6 Cln Cln Cln ClnCln Cln ALL % Cln ASC % Cln RS % Cln ST1,2 % Cln ST3,4 % ALL valid ASCvalid RS valid ST1,2 valid ST3,4 valid Oligo % up up % up up % up up %up up % up up DEX ID Name n = 38 n = 38 n = 23 n = 23 n = 15 n = 15 n =20 n = 20 n = 18 n = 18 DEX0455_010.nt.1 37415.0 52.6 52.6 69.6 69.626.7 26.7 50.0 50.0 55.6 55.6 DEX0455_011.nt.1 35317.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.1 34334.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 DEX0455_012.nt.1 34335.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_012.nt.1 34343.0 5.3 5.7 4.3 4.5 6.7 7.7 0.0 0.0 11.112.5 DEX0455_012.nt.1 34368.0 7.9 7.9 8.7 8.7 6.7 6.7 5.0 5.0 11.1 11.1DEX0455_012.nt.1 34369.0 7.9 7.9 8.7 8.7 6.7 6.7 5.0 5.0 11.1 11.1DEX0455_012.nt.2 34334.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.2 34335.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.2 34343.0 5.3 5.7 4.3 4.5 6.7 7.7 0.0 0.0 11.1 12.5DEX0455_012.nt.2 34368.0 7.9 7.9 8.7 8.7 6.7 6.7 5.0 5.0 11.1 11.1DEX0455_012.nt.2 34369.0 7.9 7.9 8.7 8.7 6.7 6.7 5.0 5.0 11.1 11.1DEX0455_017.nt.1 21032.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_024.nt.1 17957.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_028.nt.1 30821.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_028.nt.1 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 30820.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_029.nt.1 30821.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_029.nt.1 30824.0 7.9 7.9 8.7 8.7 6.7 6.7 10.0 10.0 5.6 5.6DEX0455_029.nt.1 30869.0 18.4 18.4 17.4 17.4 20.0 20.0 15.0 15.0 22.222.2 DEX0455_029.nt.1 41117.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 41151.0 10.5 10.5 13.0 13.0 6.7 6.7 15.0 15.0 5.6 5.6DEX0455_029.nt.1 41152.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_029.nt.2 30820.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_029.nt.2 30821.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_029.nt.2 30824.0 7.9 7.9 8.7 8.7 6.7 6.7 10.0 10.0 5.6 5.6DEX0455_029.nt.2 30922.0 10.5 10.5 13.0 13.0 6.7 6.7 15.0 15.0 5.6 5.6DEX0455_029.nt.2 41117.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.2 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.2 41151.0 10.5 10.5 13.0 13.0 6.7 6.7 15.0 15.0 5.6 5.6DEX0455_029.nt.2 41152.0 2.6 2.6 0.0 0.0 6.7 6.7 5.0 5.0 0.0 0.0DEX0455_034.nt.1 16423.0 2.6 3.1 0.0 0.0 6.7 9.1 0.0 0.0 5.6 6.2DEX0455_049.nt.1 36902.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_049.nt.2 36901.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_049.nt.2 36902.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_049.nt.3 36901.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_049.nt.3 36902.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_049.nt.4 36901.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_049.nt.4 36902.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_049.nt.5 36901.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_049.nt.5 36902.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.1 19803.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_061.nt.1 19804.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_061.nt.2 19803.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_061.nt.2 19804.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_061.nt.3 19803.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_061.nt.3 19804.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_061.nt.4 19803.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_061.nt.4 19804.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1DEX0455_061.nt.5 19803.0 2.6 2.6 4.3 4.3 0.0 0.0 0.0 0.0 5.6 5.6DEX0455_061.nt.5 19804.0 5.3 5.3 4.3 4.3 6.7 6.7 0.0 0.0 11.1 11.1

TABLE 7 Cln Cln Cln Cln Cln TS NOT Cln GR1,2 Cln GR3 TS up TS Cln NOTGR1,2 % valid GR3 % valid up % valid up TS up Oligo % up up % up up % upup % up % valid DEX ID Name n = 28 n = 28 n = 10 n = 10 n = 13 n = 13 n= 25 up n = 25 DEX0455_010.nt.1 37415.0 46.4 46.4 70.0 70.0 46.2 46.256.0 56.0 DEX0455_011.nt.1 35317.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.1 34334.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.1 34335.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.1 34343.0 3.6 3.7 10.0 12.5 15.4 15.4 0.0 0.0DEX0455_012.nt.1 34368.0 7.1 7.1 10.0 10.0 15.4 15.4 4.0 4.0DEX0455_012.nt.1 34369.0 7.1 7.1 10.0 10.0 15.4 15.4 4.0 4.0DEX0455_012.nt.2 34334.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.2 34335.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.2 34343.0 3.6 3.7 10.0 12.5 15.4 15.4 0.0 0.0DEX0455_012.nt.2 34368.0 7.1 7.1 10.0 10.0 15.4 15.4 4.0 4.0DEX0455_012.nt.2 34369.0 7.1 7.1 10.0 10.0 15.4 15.4 4.0 4.0DEX0455_017.nt.1 21032.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_024.nt.1 17957.0 7.1 7.1 0.0 0.0 7.7 7.7 4.0 4.0DEX0455_028.nt.1 30821.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_028.nt.1 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 30820.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_029.nt.1 30821.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_029.nt.1 30824.0 10.7 10.7 0.0 0.0 15.4 15.4 4.0 4.0DEX0455_029.nt.1 30869.0 17.9 17.9 20.0 20.0 30.8 30.8 12.0 12.0DEX0455_029.nt.1 41117.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.1 41151.0 14.3 14.3 0.0 0.0 15.4 15.4 8.0 8.0DEX0455_029.nt.1 41152.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_029.nt.2 30820.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_029.nt.2 30821.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_029.nt.2 30824.0 10.7 10.7 0.0 0.0 15.4 15.4 4.0 4.0DEX0455_029.nt.2 30922.0 14.3 14.3 0.0 0.0 15.4 15.4 8.0 8.0DEX0455_029.nt.2 41117.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.2 41120.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_029.nt.2 41151.0 14.3 14.3 0.0 0.0 15.4 15.4 8.0 8.0DEX0455_029.nt.2 41152.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_034.nt.1 16423.0 0.0 0.0 10.0 12.5 7.7 8.3 0.0 0.0DEX0455_049.nt.1 36902.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_049.nt.2 36901.0 3.6 3.6 10.0 10.0 15.4 15.4 0.0 0.0DEX0455_049.nt.2 36902.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_049.nt.3 36901.0 3.6 3.6 10.0 10.0 15.4 15.4 0.0 0.0DEX0455_049.nt.3 36902.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_049.nt.4 36901.0 3.6 3.6 10.0 10.0 15.4 15.4 0.0 0.0DEX0455_049.nt.4 36902.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_049.nt.5 36901.0 3.6 3.6 10.0 10.0 15.4 15.4 0.0 0.0DEX0455_049.nt.5 36902.0 3.6 3.6 0.0 0.0 7.7 7.7 0.0 0.0DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.1 19803.0 0.0 0.0 10.0 10.0 0.0 0.0 4.0 4.0DEX0455_061.nt.1 19804.0 0.0 0.0 20.0 20.0 7.7 7.7 4.0 4.0DEX0455_061.nt.2 19803.0 0.0 0.0 10.0 10.0 0.0 0.0 4.0 4.0DEX0455_061.nt.2 19804.0 0.0 0.0 20.0 20.0 7.7 7.7 4.0 4.0DEX0455_061.nt.3 19803.0 0.0 0.0 10.0 10.0 0.0 0.0 4.0 4.0DEX0455_061.nt.3 19804.0 0.0 0.0 20.0 20.0 7.7 7.7 4.0 4.0DEX0455_061.nt.4 19803.0 0.0 0.0 10.0 10.0 0.0 0.0 4.0 4.0DEX0455_061.nt.4 19804.0 0.0 0.0 20.0 20.0 7.7 7.7 4.0 4.0DEX0455_061.nt.5 19803.0 0.0 0.0 10.0 10.0 0.0 0.0 4.0 4.0DEX0455_061.nt.5 19804.0 0.0 0.0 20.0 20.0 7.7 7.7 4.0 4.0

TABLE 8 Cln Cln Cln Cln Multi- Cln Multi- Cln Multi- Multi- CancerMulti- Cancer Multi- Cancer Cancer ALL Cancer ASC Cancer RS Oligo ALL %up % valid ASC % up % valid RS % up % valid DEX ID Name n = 27 up n = 27n = 14 up n = 14 n = 13 up n = 13 DEX0455_002.nt.1 79699.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_002.nt.1 79700.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_002.nt.1 79700.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.196339.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 96339.1 7.4 33.3 14.366.7 0.0 0.0 DEX0455_004.nt.1 96340.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 96340.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105991.0 3.7 20.0 7.1 50.0 0.0 0.0 DEX0455_004.nt.1 105991.1 3.7 25.07.1 33.3 0.0 0.0 DEX0455_004.nt.1 105992.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105992.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105996.0 3.7 3.7 7.1 7.1 0.0 0.0 DEX0455_004.nt.1 105996.1 7.4 7.4 7.17.1 7.7 7.7 DEX0455_004.nt.2 96339.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 96339.1 7.4 33.3 14.3 66.7 0.0 0.0 DEX0455_004.nt.296340.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 96340.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.2 105991.0 3.7 20.0 7.1 50.0 0.0 0.0DEX0455_004.nt.2 105991.1 3.7 25.0 7.1 33.3 0.0 0.0 DEX0455_004.nt.2105992.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105992.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 105996.0 3.7 3.7 7.1 7.1 0.0 0.0DEX0455_004.nt.2 105996.1 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_011.nt.135317.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_011.nt.1 35317.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_012.nt.1 34334.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.1 34334.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.134335.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.1 34335.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_012.nt.2 34334.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_012.nt.2 34334.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.234335.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_012.nt.2 34335.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_017.nt.1 36482.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_017.nt.1 36482.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_033.nt.1 2023.07.4 7.4 14.3 14.3 0.0 0.0 DEX0455_033.nt.1 5327.0 3.7 3.8 7.1 7.7 0.00.0 DEX0455_033.nt.1 5328.0 3.7 3.7 7.1 7.1 0.0 0.0 DEX0455_035.nt.178519.0 51.9 51.9 50.0 50.0 53.8 53.8 DEX0455_035.nt.1 78519.1 44.4 46.242.9 46.2 46.2 46.2 DEX0455_035.nt.1 78520.0 33.3 33.3 42.9 42.9 23.123.1 DEX0455_035.nt.1 78520.1 33.3 33.3 42.9 42.9 23.1 23.1DEX0455_035.nt.2 78519.0 51.9 51.9 50.0 50.0 53.8 53.8 DEX0455_035.nt.278519.1 44.4 46.2 42.9 46.2 46.2 46.2 DEX0455_035.nt.2 78520.0 33.3 33.342.9 42.9 23.1 23.1 DEX0455_035.nt.2 78520.1 33.3 33.3 42.9 42.9 23.123.1 DEX0455_035.nt.3 78519.0 51.9 51.9 50.0 50.0 53.8 53.8DEX0455_035.nt.3 78519.1 44.4 46.2 42.9 46.2 46.2 46.2 DEX0455_035.nt.378520.0 33.3 33.3 2.9 42.9 23.1 23.1 DEX0455_035.nt.3 78520.1 33.3 33.342.9 42.9 23.1 23.1 DEX0455_038.nt.1 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.1 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.123543.0 3.7 3.7 0.0 0.0 7.7 7.7 DEX0455_038.nt.1 23543.1 3.7 3.7 0.0 0.07.7 7.7 DEX0455_038.nt.2 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.2 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.223543.0 3.7 3.7 0.0 0.0 7.7 7.7 DEX0455_038.nt.2 23543.1 3.7 3.7 0.0 0.07.7 7.7 DEX0455_038.nt.3 23542.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.3 23542.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.323543.0 3.7 3.7 0.0 0.0 7.7 7.7 DEX0455_038.nt.3 23543.1 3.7 3.7 0.0 0.07.7 7.7 DEX0455_047.nt.1 96212.0 7.4 7.4 14.3 14.3 0.0 0.0DEX0455_047.nt.1 96212.1 7.4 7.4 14.3 14.3 0.0 0.0 DEX0455_047.nt.1105764.0 7.4 8.0 14.3 14.3 0.0 0.0 DEX0455_047.nt.1 105764.1 7.4 7.414.3 14.3 0.0 0.0 DEX0455_047.nt.1 105767.0 3.7 3.7 7.1 7.1 0.0 0.0DEX0455_047.nt.1 105767.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1105768.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105768.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.2 96212.0 7.4 7.4 14.3 14.3 0.0 0.0DEX0455_047.nt.2 96212.1 7.4 7.4 14.3 14.3 0.0 0.0 DEX0455_047.nt.2105764.0 7.4 8.0 14.3 14.3 0.0 0.0 DEX0455_047.nt.2 105764.1 7.4 7.414.3 14.3 0.0 0.0 DEX0455_047.nt.2 105767.0 3.7 3.7 7.1 7.1 0.0 0.0DEX0455_047.nt.2 105767.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2105768.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105768.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_048.nt.1 1168.0 3.7 3.7 0.0 0.0 7.7 7.7DEX0455_048.nt.2 1175.0 3.7 4.0 7.1 7.7 0.0 0.0 DEX0455_050.nt.1 23378.00.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23379.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.123379.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42007.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42007.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.142008.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42008.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42008.2 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_061.nt.1 78508.0 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_061.nt.178508.1 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_061.nt.2 78508.0 7.4 7.4 7.1 7.17.7 7.7 DEX0455_061.nt.2 78508.1 7.4 7.4 7.1 7.1 7.7 7.7DEX0455_061.nt.3 78508.0 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_061.nt.378508.1 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_061.nt.4 78508.0 7.4 7.4 7.1 7.17.7 7.7 DEX0455_061.nt.4 78508.1 7.4 7.4 7.1 7.1 7.7 7.7DEX0455_061.nt.5 78508.0 7.4 7.4 7.1 7.1 7.7 7.7 DEX0455_061.nt.578508.1 7.4 7.4 7.1 7.1 7.7 7.7

Lung Cancer Chips

For lung cancer two different chip designs were evaluated withoverlapping sets of a total of 29 samples, comparing the expressionpatterns of lung cancer derived polyA+RNA to polyA+RNA isolated from apool of 12 normal lung tissues. For the Lung Array Chip all 29 samples(15 squamous cell carcinomas and 14 adenocarcinomas including 14 stage Iand 15 stage II/III cancers) were analyzed and for the Multi-CancerArray Chip a subset of 22 of these samples (10 squamous cell carcinomas,12 adenocarcinomas) were assessed.

The results for the statistically significant up-regulated genes on theLung Array Chip are shown in Table 9. The results for the statisticallysignificant up-regulated genes on the Multi-Cancer Array Chip are shownin Table 10. The first two columns of each table contain informationabout the sequence itself (DEX ID, Oligo Name), the next columns showthe results obtained for all (“ALL”) lung cancer samples, squamous cellcarcinomas (“SQ”), adenocarcinomas (“AD”), or cancers corresponding tostage I (“ST1”), or stages II and III (“ST-2,3”). ‘% up’ indicates thepercentage of all experiments in which up-regulation of at least 2-foldwas observed (n=29 for Lung Array Chip, n=22 for Multi-Cancer ArrayChip), ‘% valid up’ indicates the percentage of experiments with validexpression values in which up-regulation of at least 2-fold wasobserved. TABLE 9 Lng Lng Lng Lng Lng Lng ALL % Lng SQ % Lng AD % LngST1 % Lng ST2,3 % ALL valid SQ valid AD valid ST1 valid ST2,3 validOligo % up up % up up % up up % up up % up up DEX ID Name n = 29 n = 29n = 15 n = 15 n = 14 n = 14 n = 14 n = 14 n = 15 n = 15 DEX0455_010.nt.1791.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_010.nt.1 2720.00.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_010.nt.1 2721.0 0.0 0.00.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_010.nt.2 791.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 0.0 0.0 DEX0455_010.nt.2 2720.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 0.0 0.0 DEX0455_010.nt.2 2721.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_032.nt.1 2688.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_032.nt.1 2689.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_032.nt.1 5313.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_033.nt.1 2006.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_033.nt.1 2007.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_033.nt.1 2022.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_033.nt.1 2032.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_042.nt.1 889.0 93.1 93.1 100.0 100.0 85.7 85.7 92.9 92.9 93.393.3 DEX0455_048.nt.1 1009.0 3.4 3.4 6.7 6.7 0.0 0.0 0.0 0.0 6.7 6.7DEX0455_048.nt.1 1010.0 6.9 6.9 13.3 13.3 0.0 0.0 0.0 0.0 13.3 13.3DEX0455_048.nt.1 1011.0 6.9 6.9 13.3 13.3 0.0 0.0 7.1 7.1 6.7 6.7DEX0455_048.nt.1 1169.0 3.4 3.4 6.7 6.7 0.0 0.0 0.0 0.0 6.7 6.7DEX0455_048.nt.2 1009.0 3.4 3.4 6.7 6.7 0.0 0.0 0.0 0.0 6.7 6.7DEX0455_048.nt.2 1010.0 6.9 6.9 13.3 13.3 0.0 0.0 0.0 0.0 13.3 13.3DEX0455_048.nt.2 1011.0 6.9 6.9 13.3 13.3 0.0 0.0 7.1 7.1 6.7 6.7DEX0455_048.nt.2 1169.0 3.4 3.4 6.7 6.7 0.0 0.0 0.0 0.0 6.7 6.7DEX0455_048.nt.2 1174.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 7815.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42008.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 1582.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 1583.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 2661.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 3143.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 3160.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 3161.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 3164.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.1 3165.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 1582.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 1583.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 2661.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 3160.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 3161.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 3164.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_056.nt.2 3165.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_057.nt.1 7612.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_057.nt.1 7613.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_057.nt.2 7612.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_057.nt.2 7613.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

TABLE 10 Lng Lng Lng Lng Multi- Lng Multi- Lng Multi- Multi- CancerMulti- Cancer Multi- Cancer Cancer ALL Cancer SQ cancer AD Oligo ALL %up % valid SQ % up % valid AD % up % valid DEX ID Name n = 22 up n = 22n = 10 up n = 10 n = 12 up n = 12 DEX0455_002.nt.1 79699.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_002.nt.1 79700.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_002.nt.1 79700.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.196339.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 96339.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.1 96340.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 96340.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105991.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105991.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.1 105992.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105992.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105996.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105996.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 96339.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 96339.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.296340.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 96340.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_004.nt.2 105991.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 105991.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2105992.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105992.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 105996.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 105996.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_011.nt.135317.0 9.1 13.3 0.0 0.0 16.7 18.2 DEX0455_011.nt.1 35317.1 9.1 13.3 0.00.0 16.7 18.2 DEX0455_012.nt.1 34334.0 13.6 13.6 10.0 10.0 16.7 16.7DEX0455_012.nt.1 34334.1 13.6 13.6 10.0 10.0 16.7 16.7 DEX0455_012.nt.134335.0 13.6 13.6 10.0 10.0 16.7 16.7 DEX0455_012.nt.1 34335.1 13.6 13.610.0 10.0 16.7 16.7 DEX0455_012.nt.2 34334.0 13.6 13.6 10.0 10.0 16.716.7 DEX0455_012.nt.2 34334.1 13.6 13.6 10.0 10.0 16.7 16.7DEX0455_012.nt.2 34335.0 13.6 13.6 10.0 10.0 16.7 16.7 DEX0455_012.nt.234335.1 13.6 13.6 10.0 10.0 16.7 16.7 DEX0455_017.nt.1 36482.0 4.5 4.50.0 0.0 8.3 8.3 DEX0455_017.nt.1 36482.1 4.5 4.5 0.0 0.0 8.3 8.3DEX0455_033.nt.1 2023.0 4.5 4.5 10.0 10.0 0.0 0.0 DEX0455_033.nt.15327.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_033.nt.1 5328.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_035.nt.1 78519.0 50.0 50.0 40.0 40.0 58.3 58.3DEX0455_035.nt.1 78519.1 50.0 50.0 40.0 40.0 58.3 58.3 DEX0455_035.nt.178520.0 40.9 40.9 30.0 30.0 50.0 50.0 DEX0455_035.nt.1 78520.1 45.5 45.540.0 40.0 50.0 50.0 DEX0455_035.nt.2 78519.0 50.0 50.0 40.0 40.0 58.358.3 DEX0455_035.nt.2 78519.1 50.0 50.0 40.0 40.0 58.3 58.3DEX0455_035.nt.2 78520.0 40.9 40.9 30.0 30.0 50.0 50.0 DEX0455_035.nt.278520.1 45.5 45.5 40.0 40.0 50.0 50.0 DEX0455_035.nt.3 78519.0 50.0 50.040.0 40.0 58.3 58.3 DEX0455_035.nt.3 78519.1 50.0 50.0 40.0 40.0 58.358.3 DEX0455_035.nt.3 78520.0 40.9 40.9 30.0 30.0 50.0 50.0DEX0455_035.nt.3 78520.1 45.5 45.5 40.0 40.0 50.0 50.0 DEX0455_038.nt.123542.0 4.5 4.5 0.0 0.0 8.3 8.3 DEX0455_038.nt.1 23542.1 9.1 9.1 0.0 0.016.7 16.7 DEX0455_038.nt.1 23543.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.1 23543.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.223542.0 4.5 4.5 0.0 0.0 8.3 8.3 DEX0455_038.nt.2 23542.1 9.1 9.1 0.0 0.016.7 16.7 DEX0455_038.nt.2 23543.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.2 23543.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.323542.0 4.5 4.5 0.0 0.0 8.3 8.3 DEX0455_038.nt.3 23542.1 9.1 9.1 0.0 0.016.7 16.7 DEX0455_038.nt.3 23543.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_038.nt.3 23543.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.196212.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 96212.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_047.nt.1 105764.0 4.5 5.0 10.0 12.5 0.0 0.0DEX0455_047.nt.1 105764.1 4.5 5.0 10.0 11.1 0.0 0.0 DEX0455_047.nt.1105767.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105767.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.1 105768.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.1 105768.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.296212.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 96212.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_047.nt.2 105764.0 4.5 5.0 10.0 12.5 0.0 0.0DEX0455_047.nt.2 105764.1 4.5 5.0 10.0 11.1 0.0 0.0 DEX0455_047.nt.2105767.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105767.1 0.0 0.0 0.00.0 0.0 0.0 DEX0455_047.nt.2 105768.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_047.nt.2 105768.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_048.nt.11168.0 4.5 4.5 10.0 10.0 0.0 0.0 DEX0455_048.nt.2 1175.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.123379.0 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23379.1 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42007.0 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.1 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.142007.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42008.0 0.0 0.0 0.0 0.00.0 0.0 DEX0455_050.nt.1 42008.1 0.0 0.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42008.2 0.0 0.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.178508.0 31.8 31.8 30.0 30.0 33.3 33.3 DEX0455_061.nt.1 78508.1 31.8 31.820.0 20.0 41.7 41.7 DEX0455_061.nt.2 78508.0 31.8 31.8 30.0 30.0 33.333.3 DEX0455_061.nt.2 78508.1 31.8 31.8 20.0 20.0 41.7 41.7DEX0455_061.nt.3 78508.0 31.8 31.8 30.0 30.0 33.3 33.3 DEX0455_061.nt.378508.1 31.8 31.8 20.0 20.0 41.7 41.7 DEX0455_061.nt.4 78508.0 31.8 31.830.0 30.0 33.3 33.3 DEX0455_061.nt.4 78508.1 31.8 31.8 20.0 20.0 41.741.7 DEX0455_061.nt.5 78508.0 31.8 31.8 30.0 30.0 33.3 33.3DEX0455_061.nt.5 78508.1 31.8 31.8 20.0 20.0 41.7 41.7

Prostate Cancer

For prostate cancer three different chip designs were evaluated withoverlapping sets of a total of 29 samples, comparing the expressionpatterns of prostate cancer or benign disease derived total RNA to totalRNA isolated from a pool of 35 normal prostate tissues. For theProstate1 Array and Prostate2 Array Chips all 29 samples (17 prostatecancer samples, 12 non-malignant disease samples) were analyzed. For theMulti-Cancer Array Chip a subset of 28 of these samples (16 prostatecancer samples, 12 non-malignant disease samples) were analyzed.

The results for the statistically significant up-regulated genes on theProstate1 Array Chip and the Prostate2 Array Chip are shown in Table 11.The results for the statistically significant up-regulated genes on theMulti-Cancer Array Chip are shown in Table 12. The first two columns ofeach table contain information about the sequence itself (DEX ID, OligoName), the next columns show the results obtained for prostate cancersamples (“CAN”) or non-malignant disease samples (“DIS”). ‘% up’indicates the percentage of all experiments in which up-regulation of atleast 2-fold was observed (n=29 for the Prostate2 Array Chip and theMulti-Cancer Array Chip), ‘% valid up’ indicates the percentage ofexperiments with valid expression values in which up-regulation of atleast 2-fold was observed. TABLE 11 Pro Pro DIS CAN Pro CAN Pro DIS %valid Oligo % up % valid up % up up DEX ID Name n = 17 n = 17 n = 12 n =12 DEX0455_010.nt.1 28129.01 0.0 0.0 0.0 0.0 DEX0455_010.nt.1 28129.020.0 0.0 8.3 8.3 DEX0455_010.nt.2 28129.01 0.0 0.0 0.0 0.0DEX0455_010.nt.2 28129.02 0.0 0.0 8.3 8.3 DEX0455_023.nt.1 8770.01 0.00.0 0.0 0.0 DEX0455_023.nt.1 8770.02 0.0 0.0 0.0 0.0 DEX0455_023.nt.18770.03 0.0 0.0 0.0 0.0 DEX0455_034.nt.1 26867.01 0.0 0.0 0.0 0.0DEX0455_034.nt.1 26867.02 0.0 0.0 0.0 0.0 DEX0455_034.nt.1 32554.01 0.00.0 0.0 0.0 DEX0455_034.nt.1 32554.02 5.9 5.9 8.3 8.3 DEX0455_034.nt.132554.03 5.9 7.1 0.0 0.0 DEX0455_034.nt.1 32558.01 0.0 0.0 0.0 0.0DEX0455_034.nt.1 32558.02 0.0 0.0 0.0 0.0 DEX0455_034.nt.1 32558.03 0.00.0 0.0 0.0 DEX0455_038.nt.1 23492.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.123492.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 23542.01 0.0 0.0 0.0 0.0DEX0455_038.nt.1 23542.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 23546.01 5.933.3 0.0 0.0 DEX0455_038.nt.1 23546.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.124418.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 24418.02 0.0 0.0 0.0 0.0DEX0455_038.nt.1 24422.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 24422.02 0.00.0 0.0 0.0 DEX0455_038.nt.1 27965.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.127965.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 28535.01 0.0 0.0 0.0 0.0DEX0455_038.nt.1 28535.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23492.01 0.00.0 0.0 0.0 DEX0455_038.nt.2 23492.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.223542.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23542.02 0.0 0.0 0.0 0.0DEX0455_038.nt.2 23684.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23684.02 0.00.0 0.0 0.0 DEX0455_038.nt.2 24418.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.224418.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 27965.01 0.0 0.0 0.0 0.0DEX0455_038.nt.2 27965.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 28535.01 0.00.0 0.0 0.0 DEX0455_038.nt.2 28535.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.323492.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.3 23492.02 0.0 0.0 0.0 0.0DEX0455_038.nt.3 23542.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.3 23542.02 0.00.0 0.0 0.0 DEX0455_038.nt.3 27965.01 0.0 0.0 0.0 0.0 DEX0455_038.nt.327965.02 0.0 0.0 0.0 0.0 DEX0455_038.nt.3 28535.01 0.0 0.0 0.0 0.0DEX0455_038.nt.3 28535.02 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23378.01 0.00.0 0.0 0.0 DEX0455_050.nt.1 23378.02 5.9 11.1 0.0 0.0 DEX0455_057.nt.133332.01 0.0 0.0 0.0 0.0 DEX0455_057.nt.1 33332.02 0.0 0.0 0.0 0.0DEX0455_057.nt.2 33332.01 0.0 0.0 0.0 0.0 DEX0455_057.nt.2 33332.02 0.00.0 0.0 0.0

TABLE 12 Pro Multi Pro Multi- Pro Multi- Cancer CAN Pro Multi- CancerDIS Oligo Cancer CAN % valid up Cancer DIS % valid up DEX ID Name % up n= 16 n = 16 % up n = 12 n = 12 DEX0455_002.nt.1 79699.1 0.0 0.0 0.0 0.0DEX0455_002.nt.1 79700.0 0.0 0.0 0.0 0.0 DEX0455_002.nt.1 79700.1 0.00.0 0.0 0.0 DEX0455_004.nt.1 96339.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.196339.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 96340.0 0.0 0.0 0.0 0.0DEX0455_004.nt.1 96340.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105991.0 0.00.0 0.0 0.0 DEX0455_004.nt.1 105991.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.1105992.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105992.1 0.0 0.0 0.0 0.0DEX0455_004.nt.1 105996.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.1 105996.1 0.00.0 0.0 0.0 DEX0455_004.nt.2 96339.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.296339.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 96340.0 0.0 0.0 0.0 0.0DEX0455_004.nt.2 96340.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105991.0 0.00.0 0.0 0.0 DEX0455_004.nt.2 105991.1 0.0 0.0 0.0 0.0 DEX0455_004.nt.2105992.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105992.1 0.0 0.0 0.0 0.0DEX0455_004.nt.2 105996.0 0.0 0.0 0.0 0.0 DEX0455_004.nt.2 105996.1 0.00.0 0.0 0.0 DEX0455_011.nt.1 35317.0 0.0 0.0 0.0 0.0 DEX0455_011.nt.135317.1 0.0 0.0 0.0 0.0 DEX0455_012.nt.1 34334.0 17.6 18.8 0.0 0.0DEX0455_012.nt.1 34334.1 23.5 25.0 0.0 0.0 DEX0455_012.nt.1 34335.0 23.526.7 8.3 8.3 DEX0455_012.nt.1 34335.1 17.6 18.8 0.0 0.0 DEX0455_012.nt.234334.0 17.6 18.8 0.0 0.0 DEX0455_012.nt.2 34334.1 23.5 25.0 0.0 0.0DEX0455_012.nt.2 34335.0 23.5 26.7 8.3 8.3 DEX0455_012.nt.2 34335.1 17.618.8 0.0 0.0 DEX0455_017.nt.1 36482.0 5.9 6.7 0.0 0.0 DEX0455_017.nt.136482.1 5.9 6.2 0.0 0.0 DEX0455_033.nt.1 2023.0 0.0 0.0 0.0 0.0DEX0455_033.nt.1 5327.0 0.0 0.0 0.0 0.0 DEX0455_033.nt.1 5328.0 0.0 0.00.0 0.0 DEX0455_035.nt.1 78519.0 0.0 0.0 0.0 0.0 DEX0455_035.nt.178519.1 0.0 0.0 0.0 0.0 DEX0455_035.nt.1 78520.0 0.0 0.0 0.0 0.0DEX0455_035.nt.1 78520.1 0.0 0.0 0.0 0.0 DEX0455_035.nt.2 78519.0 0.00.0 0.0 0.0 DEX0455_035.nt.2 78519.1 0.0 0.0 0.0 0.0 DEX0455_035.nt.278520.0 0.0 0.0 0.0 0.0 DEX0455_035.nt.2 78520.1 0.0 0.0 0.0 0.0DEX0455_035.nt.3 78519.0 0.0 0.0 0.0 0.0 DEX0455_035.nt.3 78519.1 0.00.0 0.0 0.0 DEX0455_035.nt.3 78520.0 0.0 0.0 0.0 0.0 DEX0455_035.nt.378520.1 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 23542.0 0.0 0.0 0.0 0.0DEX0455_038.nt.1 23542.1 0.0 0.0 0.0 0.0 DEX0455_038.nt.1 23543.0 0.00.0 0.0 0.0 DEX0455_038.nt.1 23543.1 0.0 0.0 0.0 0.0 DEX0455_038.nt.223542.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23542.1 0.0 0.0 0.0 0.0DEX0455_038.nt.2 23543.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.2 23543.1 0.00.0 0.0 0.0 DEX0455_038.nt.3 23542.0 0.0 0.0 0.0 0.0 DEX0455_038.nt.323542.1 0.0 0.0 0.0 0.0 DEX0455_038.nt.3 23543.0 0.0 0.0 0.0 0.0DEX0455_038.nt.3 23543.1 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 96212.0 0.00.0 0.0 0.0 DEX0455_047.nt.1 96212.1 0.0 0.0 0.0 0.0 DEX0455_047.nt.1105764.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105764.1 0.0 0.0 0.0 0.0DEX0455_047.nt.1 105767.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1 105767.1 0.00.0 0.0 0.0 DEX0455_047.nt.1 105768.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.1105768.1 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 96212.0 0.0 0.0 0.0 0.0DEX0455_047.nt.2 96212.1 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105764.0 0.00.0 0.0 0.0 DEX0455_047.nt.2 105764.1 0.0 0.0 0.0 0.0 DEX0455_047.nt.2105767.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105767.1 0.0 0.0 0.0 0.0DEX0455_047.nt.2 105768.0 0.0 0.0 0.0 0.0 DEX0455_047.nt.2 105768.1 0.00.0 0.0 0.0 DEX0455_048.nt.1 1168.0 0.0 0.0 8.3 8.3 DEX0455_048.nt.21175.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23378.0 0.0 0.0 0.0 0.0DEX0455_050.nt.1 23378.1 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 23379.0 0.00.0 0.0 0.0 DEX0455_050.nt.1 23379.1 0.0 0.0 0.0 0.0 DEX0455_050.nt.142007.0 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42007.1 0.0 0.0 0.0 0.0DEX0455_050.nt.1 42007.2 0.0 0.0 0.0 0.0 DEX0455_050.nt.1 42008.0 0.00.0 0.0 0.0 DEX0455_050.nt.1 42008.1 0.0 0.0 0.0 0.0 DEX0455_050.nt.142008.2 0.0 0.0 0.0 0.0 DEX0455_061.nt.1 78508.0 0.0 0.0 0.0 0.0DEX0455_061.nt.1 78508.1 0.0 0.0 0.0 0.0 DEX0455_061.nt.2 78508.0 0.00.0 0.0 0.0 DEX0455_061.nt.2 78508.1 0.0 0.0 0.0 0.0 DEX0455_061.nt.378508.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.3 78508.1 0.0 0.0 0.0 0.0DEX0455_061.nt.4 78508.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.4 78508.1 0.00.0 0.0 0.0 DEX0455_061.nt.5 78508.0 0.0 0.0 0.0 0.0 DEX0455_061.nt.578508.1 0.0 0.0 0.0 0.0SEQ ID NO: 1-128 was up-regulated on various tissue microarrays.Accordingly, nucleotide SEQ ID NO: 1-128 or the encoded protein SEQ IDNO: 129-295 may be used as a cancer therapeutic and/or diagnostic targetfor the tissues in which expression is shown.

The following table lists the location (Oligo Location) where themicroarray oligos (Oligo ID) map on the transcripts (DEX ID) of thepresent invention. Each Oligo ID may have been printed multiple times ona single chip as replicates. The Oligo Name is an exemplary replicate(e.g. 1000.01) for the Oligo ID (e.g. 1000), and data from otherreplicates (e.g. 1000.02, 1000.03) may be reported. Additionally, theArray (Chip Name) that each oligo and oligo replicates were printed onis included. DEX NT ID Oligo ID Oligo Name Chip Name Oligo LocationDEX0455_001.nt.1 34930 34930.01 Ovarian array 4736-4795 DEX0455_002.nt.121577 21577.02 Ovarian array 198-257 DEX0455_002.nt.1 79699 79699.0Multi-Cancer array 1430-1489 DEX0455_002.nt.1 21553 21553.01 Ovarianarray 513-572 DEX0455_002.nt.1 79700 79700.0 Multi-Cancer array1429-1488 DEX0455_003.nt.1 17466 17466.02 Ovarian array 1075-1134DEX0455_004.nt.1 96340 96340.0 Multi-Cancer array 6807-6866DEX0455_004.nt.1 96339 96339.0 Multi-Cancer array 6906-6965DEX0455_004.nt.1 105991 105991.0 Multi-Cancer array 6906-6965DEX0455_004.nt.1 105992 105992.0 Multi-Cancer array 6807-6866DEX0455_004.nt.1 105996 105996.0 Multi-Cancer array 8462-8521DEX0455_004.nt.2 96340 96340.0 Multi-Cancer array 5651-5710DEX0455_004.nt.2 105991 105991.0 Multi-Cancer array 5750-5809DEX0455_004.nt.2 105992 105992.0 Multi-Cancer array 5651-5710DEX0455_004.nt.2 105996 105996.0 Multi-Cancer array 7306-7365DEX0455_004.nt.2 96339 96339.0 Multi-Cancer array 5750-5809DEX0455_005.nt.1 24874 24874.01 Ovarian array 475-534 DEX0455_005.nt.120619 20619.02 Ovarian array 472-531 DEX0455_005.nt.2 24874 24874.01Ovarian array 475-534 DEX0455_007.nt.1 30109 30109.01 Ovarian array 982-1041 DEX0455_008.nt.1 22387 22387.01 Ovarian array 1666-1725DEX0455_008.nt.1 18508 18508.02 Ovarian array 1193-1252 DEX0455_009.nt.19720 9720.02 Ovarian array 1745-1804 DEX0455_010.nt.1 2721 2721.0 Lungarray 501-560 DEX0455_010.nt.1 37415 37415.0 Colon array 1040-1099DEX0455_010.nt.1 32151 32151.0 Breast array 748-807 DEX0455_010.nt.12720 2720.0 Lung array 542-601 DEX0455_010.nt.1 21675 21675.02 Ovarianarray  965-1024 DEX0455_010.nt.1 20627 20627.02 Ovarian array 250-309DEX0455_010.nt.1 28129 28129.02 Prostate1 array  964-1023DEX0455_010.nt.1 791 791.0 Lung array 1045-1104 DEX0455_010.nt.2 27202720.0 Lung array 379-438 DEX0455_010.nt.2 32151 32151.0 Breast array585-644 DEX0455_010.nt.2 28129 28129.02 Prostate1 array 801-860DEX0455_010.nt.2 37415 37415.0 Colon array 877-936 DEX0455_010.nt.221675 21675.02 Ovarian array 802-861 DEX0455_010.nt.2 791 791.0 Lungarray 882-941 DEX0455_010.nt.2 2721 2721.0 Lung array 338-397DEX0455_011.nt.1 35317 35317.0 Colon array 398-457 DEX0455_012.nt.134368 34368.0 Colon array 2484-2543 DEX0455_012.nt.1 34369 34369.0 Colonarray 2441-2500 DEX0455_012.nt.1 34334 34334.0 Colon array 3108-3167DEX0455_012.nt.1 34343 34343.0 Colon array 472-531 DEX0455_012.nt.134335 34335.0 Colon array 3022-3081 DEX0455_012.nt.2 34334 34334.0 Colonarray 2527-2586 DEX0455_012.nt.2 34343 34343.0 Colon array 472-531DEX0455_012.nt.2 34369 34369.0 Colon array 1860-1919 DEX0455_012.nt.234335 34335.0 Colon array 2441-2500 DEX0455_012.nt.2 34368 34368.0 Colonarray 1903-1962 DEX0455_013.nt.1 9838 9838.02 Ovarian array 1304-1363DEX0455_014.nt.1 10624 10624.02 Ovarian array 1832-1891 DEX0455_014.nt.114604 14604.01 Ovarian array 925-984 DEX0455_015.nt.1 19518 19518.01Ovarian array 277-336 DEX0455_016.nt.1 23734 23734.02 Ovarian array531-590 DEX0455_017.nt.1 28221 28221.0 Breast array 679-738DEX0455_017.nt.1 21032 21032.0 Colon array 314-373 DEX0455_017.nt.136482 36482.0 Multi-Cancer array 314-373 DEX0455_018.nt.1 21575 21575.01Ovarian array 1516-1575 DEX0455_018.nt.1 21571 21571.02 Ovarian array623-682 DEX0455_018.nt.1 21609 21609.02 Ovarian array 933-992DEX0455_018.nt.2 21575 21575.01 Ovarian array 2287-2346 DEX0455_019.nt.120669 20669.01 Ovarian array 615-674 DEX0455_021.nt.1 23780 23780.01Ovarian array 517-576 DEX0455_021.nt.1 21469 21469.02 Ovarian array430-489 DEX0455_021.nt.1 21433 21433.01 Ovarian array 518-577DEX0455_021.nt.1 21475 21475.01 Ovarian array 517-576 DEX0455_021.nt.221469 21469.02 Ovarian array 1528-1587 DEX0455_021.nt.2 21475 21475.01Ovarian array 1615-1674 DEX0455_021.nt.2 21433 21433.01 Ovarian array1616-1675 DEX0455_021.nt.2 23780 23780.01 Ovarian array 1615-1674DEX0455_021.nt.3 21433 21433.01 Ovarian array 1859-1918 DEX0455_021.nt.321475 21475.01 Ovarian array 1858-1917 DEX0455_021.nt.3 21469 21469.02Ovarian array 1771-1830 DEX0455_021.nt.3 23780 23780.01 Ovarian array1858-1917 DEX0455_021.nt.4 21469 21469.02 Ovarian array 1914-1973DEX0455_021.nt.4 21475 21475.01 Ovarian array 2001-2060 DEX0455_021.nt.421433 21433.01 Ovarian array 2002-2061 DEX0455_022.nt.1 9920 9920.02Ovarian array 1022-1081 DEX0455_022.nt.1 20311 20311.01 Ovarian array718-777 DEX0455_022.nt.1 20299 20299.01 Ovarian array 529-588DEX0455_022.nt.1 23280 23280.0 Breast array 427-486 DEX0455_022.nt.120317 20317.02 Ovarian array 718-777 DEX0455_022.nt.2 9920 9920.02Ovarian array 1016-1075 DEX0455_022.nt.2 20311 20311.01 Ovarian array712-771 DEX0455_022.nt.2 20317 20317.02 Ovarian array 712-771DEX0455_022.nt.2 20299 20299.01 Ovarian array 552-611 DEX0455_022.nt.39920 9920.02 Ovarian array 613-672 DEX0455_022.nt.3 20317 20317.02Ovarian array 309-368 DEX0455_022.nt.3 20311 20311.01 Ovarian array309-368 DEX0455_023.nt.1 16374 16374.02 Ovarian array 2119-2178DEX0455_023.nt.1 8770 8770.03 Prostate2 array 1897-1956 DEX0455_023.nt.116378 16378.01 Ovarian array 937-996 DEX0455_023.nt.1 16187 16187.01Ovarian array 666-725 DEX0455_024.nt.1 21507 21507.01 Ovarian array2357-2416 DEX0455_024.nt.1 21487 21487.01 Ovarian array 796-855DEX0455_024.nt.1 12149 12149.01 Ovarian array 2439-2498 DEX0455_024.nt.121547 21547.02 Ovarian array 1555-1614 DEX0455_024.nt.1 17957 17957.0Colon array 2002-2061 DEX0455_024.nt.2 21507 21507.01 Ovarian array1790-1849 DEX0455_024.nt.2 12149 12149.01 Ovarian array 1872-1931DEX0455_024.nt.2 21547 21547.02 Ovarian array  988-1047 DEX0455_024.nt.217957 17957.0 Colon array 1435-1494 DEX0455_025.nt.1 12167 12167.01Ovarian array 475-534 DEX0455_025.nt.1 16964 16964.02 Ovarian array3509-3568 DEX0455_025.nt.1 16956 16956.02 Ovarian array 3533-3592DEX0455_025.nt.1 16958 16958.01 Ovarian array 808-867 DEX0455_025.nt.119010 19010.01 Ovarian array 1260-1319 DEX0455_025.nt.2 12167 12167.01Ovarian array 475-534 DEX0455_025.nt.2 16964 16964.02 Ovarian array2465-2524 DEX0455_025.nt.2 16956 16956.02 Ovarian array 2489-2548DEX0455_025.nt.2 16958 16958.01 Ovarian array 808-867 DEX0455_025.nt.219010 19010.1 Ovarian array 1260-1319 DEX0455_025.nt.3 12167 12167.01Ovarian array 475-534 DEX0455_025.nt.3 19010 19010.01 Ovarian array1260-1319 DEX0455_025.nt.3 16958 16958.01 Ovarian array 808-867DEX0455_025.nt.4 19010 19010.01 Ovarian array 1260-1319 DEX0455_025.nt.416956 16956.02 Ovarian array 2167-2226 DEX0455_025.nt.4 16964 16964.02Ovarian array 2143-2202 DEX0455_025.nt.4 12167 12167.01 Ovarian array475-534 DEX0455_027.nt.1 21549 21549.01 Ovarian array 1483-1542DEX0455_028.nt.1 41120 41120.0 Colon array 477-536 DEX0455_028.nt.130821 30821.0 Colon array 673-732 DEX0455_029.nt.1 41151 41151.0 Colonarray 2429-2488 DEX0455_029.nt.1 22113 22113.01 Ovarian array 3222-3281DEX0455_029.nt.1 30869 30869.0 Colon array 5572-5631 DEX0455_029.nt.141120 41120.0 Colon array 1984-2043 DEX0455_029.nt.1 23386 23386.01Ovarian array 2429-2488 DEX0455_029.nt.1 30820 30820.0 Colon array2388-2447 DEX0455_029.nt.1 41117 41117.0 Colon array 2296-2355DEX0455_029.nt.1 30821 30821.0 Colon array 2348-2407 DEX0455_029.nt.123400 23400.02 Ovarian array 2296-2355 DEX0455_029.nt.1 41152 41152.0Colon array 2372-2431 DEX0455_029.nt.1 17430 17430.02 Ovarian array2388-2447 DEX0455_029.nt.1 30824 30824.0 Colon array 5798-5857DEX0455_029.nt.1 17448 17448.01 Ovarian array 5798-5857 DEX0455_029.nt.241120 41120.0 Colon array 2412-2471 DEX0455_029.nt.2 17430 17430.02Ovarian array 2816-2875 DEX0455_029.nt.2 23386 23386.01 Ovarian array2857-2916 DEX0455_029.nt.2 30824 30824.0 Colon array 5101-5160DEX0455_029.nt.2 17424 17424.01 Ovarian array 4880-4939 DEX0455_029.nt.230922 30922.0 Colon array 4880-4939 DEX0455_029.nt.2 23400 23400.02Ovarian array 2724-2783 DEX0455_029.nt.2 41152 41152.0 Colon array2800-2859 DEX0455_029.nt.2 30820 30820.0 Colon array 2816-2875DEX0455_029.nt.2 22113 22113.01 Ovarian array 3650-3709 DEX0455_029.nt.241117 41117.0 Colon array 2724-2783 DEX0455_029.nt.2 41151 41151.0 Colonarray 2857-2916 DEX0455_029.nt.2 30821 30821.0 Colon array 2776-2835DEX0455_029.nt.2 17448 17448.01 Ovarian array 5101-5160 DEX0455_030.nt.117204 17204.02 Ovarian array 1225-1284 DEX0455_030.nt.1 17262 17262.02Ovarian array 1011-1070 DEX0455_030.nt.1 17278 17278.02 Ovarian array 991-1050 DEX0455_030.nt.1 11613 11613.01 Ovarian array 1011-1070DEX0455_030.nt.2 17274 17274.02 Ovarian array 696-755 DEX0455_030.nt.217204 17204.02 Ovarian array  984-1043 DEX0455_030.nt.2 17278 17278.02Ovarian array 713-772 DEX0455_030.nt.2 17262 17262.02 Ovarian array733-792 DEX0455_031.nt.1 20773 20773.02 Ovarian array 2724-2783DEX0455_032.nt.1 2688 2688.0 Lung array  952-1011 DEX0455_032.nt.1 1158511585.01 Ovarian array 1342-1401 DEX0455_032.nt.1 2689 2689.0 Lung array910-969 DEX0455_032.nt.1 18556 18556.02 Ovarian array  952-1011DEX0455_032.nt.1 5313 5313.0 Lung array 1342-1401 DEX0455_033.nt.1 53285328.0 Multi-Cancer array 402-461 DEX0455_033.nt.1 2006 2006.0 Lungarray 402-461 DEX0455_033.nt.1 2022 2022.0 Lung array 482-541DEX0455_033.nt.1 2032 2032.0 Lung array 290-349 DEX0455_033.nt.1 20072007.0 Lung array 361-420 DEX0455_033.nt.1 5327 5327.0 Multi-Cancerarray 442-501 DEX0455_033.nt.1 2023 2023.0 Multi-Cancer array 442-501DEX0455_034.nt.1 10722 10722.02 Ovarian array 2454-2513 DEX0455_034.nt.132554 32554.02 Prostate2 array 1815-1874 DEX0455_034.nt.1 21421 21421.02Ovarian array 1815-1874 DEX0455_034.nt.1 32558 32558.01 Prostate2 array1053-1112 DEX0455_034.nt.1 16423 16423.0 Colon array 885-944DEX0455_034.nt.1 21401 21401.02 Ovarian array 1053-1112 DEX0455_034.nt.126867 26867.01 Prostate1 array 2454-2513 DEX0455_035.nt.1 78519 78519.0Multi-Cancer array 923-982 DEX0455_035.nt.1 78520 78520.0 Multi-Cancerarray 857-916 DEX0455_035.nt.1 103385 103385.01 Ovarian array 926-985DEX0455_035.nt.2 78519 78519.0 Multi-Cancer array 1152-1211DEX0455_035.nt.2 103385 103385.01 Ovarian array 1155-1214DEX0455_035.nt.2 78520 78520.0 Multi-Cancer array 1086-1145DEX0455_035.nt.3 103385 103385.01 Ovarian array 1034-1093DEX0455_035.nt.3 78519 78519.0 Multi-Cancer array 1031-1090DEX0455_035.nt.3 78520 78520.0 Multi-Cancer array  965-1024DEX0455_035.nt.3 21144 21144.0 Breast array 126-185 DEX0455_035.nt.321143 21143.0 Breast array 212-271 DEX0455_036.nt.1 92327 92327.01Ovarian array 177-236 DEX0455_037.nt.1 17490 17490.01 Ovarian array894-953 DEX0455_037.nt.1 11575 11575.01 Ovarian array 892-951DEX0455_037.nt.1 17486 17486.01 Ovarian array 887-946 DEX0455_037.nt.217490 17490.01 Ovarian array 1459-1518 DEX0455_037.nt.2 11575 11575.01Ovarian array 1457-1516 DEX0455_037.nt.3 17490 17490.01 Ovarian array2399-2458 DEX0455_037.nt.3 11575 11575.01 Ovarian array 2397-2456DEX0455_037.nt.3 17486 17486.01 Ovarian array 2392-2451 DEX0455_037.nt.417490 17490.01 Ovarian array 515-574 DEX0455_037.nt.4 17486 17486.01Ovarian array 508-567 DEX0455_037.nt.4 11575 11575.01 Ovarian array513-572 DEX0455_037.nt.5 17486 17486.01 Ovarian array 571-630DEX0455_037.nt.5 17490 17490.01 Ovarian array 578-637 DEX0455_037.nt.511575 11575.01 Ovarian array 576-635 DEX0455_038.nt.1 23543 23543.0Multi-Cancer array 5011-5070 DEX0455_038.nt.1 23492 23492.02 Prostate1array 5433-5492 DEX0455_038.nt.1 23546 23546.01 Prostate1 array3874-3933 DEX0455_038.nt.1 24422 24422.01 Prostate1 array 3874-3933DEX0455_038.nt.1 23542 23542.0 Multi-Cancer array 5118-5177DEX0455_038.nt.1 24418 24418.01 Prostate1 array 2859-2918DEX0455_038.nt.1 27965 27965.01 Prostate1 array 1956-2015DEX0455_038.nt.1 28535 28535.01 Prostate1 array 5154-5213DEX0455_038.nt.2 27965 27965.01 Prostate1 array 1956-2015DEX0455_038.nt.2 23543 23543.0 Multi-Cancer array 4443-4502DEX0455_038.nt.2 28535 28535.01 Prostate1 array 4586-4645DEX0455_038.nt.2 23492 23492.02 Prostate1 array 4865-4924DEX0455_038.nt.2 24418 24418.01 Prostate1 array 2859-2918DEX0455_038.nt.2 23542 23542.0 Multi-Cancer array 4550-4609DEX0455_038.nt.2 23684 23684.02 Prostate1 array 3719-3778DEX0455_038.nt.3 23543 23543.0 Multi-Cancer array 2528-2587DEX0455_038.nt.3 23492 23492.02 Prostate1 array 2950-3009DEX0455_038.nt.3 23542 23542.0 Multi-Cancer array 2635-2694DEX0455_038.nt.3 27965 27965.01 Prostate1 array 1693-1752DEX0455_038.nt.3 28535 28535.01 Prostate1 array 2671-2730DEX0455_039.nt.1 21505 21505.02 Ovarian array 355-414 DEX0455_039.nt.211527 11527.01 Ovarian array 467-526 DEX0455_040.nt.1 21489 21489.02Ovarian array 281-340 DEX0455_040.nt.1 21501 21501.02 Ovarian array772-831 DEX0455_040.nt.1 21511 21511.01 Ovarian array 586-645DEX0455_040.nt.2 21489 21489.02 Ovarian array 698-757 DEX0455_040.nt.221511 21511.01 Ovarian array 1003-1062 DEX0455_040.nt.2 21501 21501.02Ovarian array 1189-1248 DEX0455_041.nt.1 16980 16980.01 Ovarian array125-184 DEX0455_041.nt.1 16998 16998.0 Breast array 125-184DEX0455_041.nt.1 12155 12155.01 Ovarian array 309-368 DEX0455_042.nt.1889 889.0 Lung array 346-405 DEX0455_042.nt.1 18214 18214.02 Ovarianarray 346-405 DEX0455_043.nt.1 14656 14656.02 Ovarian array 463-522DEX0455_045.nt.1 36013 36013.01 Ovarian array 382-441 DEX0455_046.nt.117314 17314.01 Ovarian array 614-673 DEX0455_046.nt.1 19072 19072.0Breast array 614-673 DEX0455_047.nt.1 105768 105768.0 Multi-Cancer array3274-3333 DEX0455_047.nt.1 96212 96212.0 Multi-Cancer array 2703-2762DEX0455_047.nt.1 105767 105767.0 Multi-Cancer array 3314-3373DEX0455_047.nt.1 105764 105764.0 Multi-Cancer array 2703-2762DEX0455_047.nt.2 105768 105768.0 Multi-Cancer array 1478-1537DEX0455_047.nt.2 105767 105767.0 Multi-Cancer array 1518-1577DEX0455_047.nt.2 96212 96212.0 Multi-Cancer array 907-966DEX0455_048.nt.1 1169 1169.0 Lung array 175-234 DEX0455_048.nt.1 10111011.0 Lung array 202-261 DEX0455_048.nt.1 1009 1009.0 Lung array192-251 DEX0455_048.nt.1 1010 1010.0 Lung array 242-301 DEX0455_048.nt.11168 1168.0 Multi-Cancer array 180-239 DEX0455_048.nt.2 1169 1169.0 Lungarray 386-445 DEX0455_048.nt.2 1011 1011.0 Lung array 413-472DEX0455_048.nt.2 1009 1009.0 Lung array 403-462 DEX0455_048.nt.2 11751175.0 Multi-Cancer array 254-313 DEX0455_048.nt.2 1168 1168.0Multi-Cancer array 391-450 DEX0455_048.nt.2 1174 1174.0 Lung array259-318 DEX0455_048.nt.2 1010 1010.0 Lung array 453-512 DEX0455_049.nt.111511 11511.02 Ovarian array 2111-2170 DEX0455_049.nt.1 36902 36902.0Colon array 928-987 DEX0455_049.nt.2 36901 36901.0 Colon array 621-680DEX0455_049.nt.2 11511 11511.02 Ovarian array 1528-1587 DEX0455_049.nt.236902 36902.0 Colon array 582-641 DEX0455_049.nt.3 36901 36901.0 Colonarray  967-1026 DEX0455_049.nt.4 11511 11511.02 Ovarian array 2102-2161DEX0455_049.nt.4 36902 36902.0 Colon array 1156-1215 DEX0455_049.nt.436901 36901.0 Colon array 1195-1254 DEX0455_049.nt.5 36902 36902.0 Colonarray 299-358 DEX0455_049.nt.5 11511 11511.02 Ovarian array 1245-1304DEX0455_050.nt.1 29736 29736.0 Breast array 171-230 DEX0455_050.nt.17815 7815.0 Lung array 385-444 DEX0455_050.nt.1 23378 23378.0 Breastarray 684-743 DEX0455_050.nt.1 42008 42008.0 Multi-Cancer array 329-388DEX0455_050.nt.1 42007 42007.0 Multi-Cancer array 329-388DEX0455_050.nt.1 22136 22136.0 Breast array 636-695 DEX0455_050.nt.123379 23379.0 Breast array 385-444 DEX0455_052.nt.1 91971 91971.01Ovarian array 1686-1745 DEX0455_054.nt.1 19799 19799.0 Breast array1918-1977 DEX0455_055.nt.1 20541 20541.01 Ovarian array 1705-1764DEX0455_055.nt.1 12731 12731.0 Breast array 1601-1660 DEX0455_055.nt.112732 12732.0 Breast array 1395-1454 DEX0455_055.nt.1 11273 11273.02Ovarian array 1815-1874 DEX0455_055.nt.2 20541 20541.01 Ovarian array1403-1462 DEX0455_055.nt.2 12731 12731.0 Breast array 1299-1358DEX0455_055.nt.2 12732 12732.0 Breast array 1136-1195 DEX0455_055.nt.211273 11273.02 Ovarian array 1513-1572 DEX0455_055.nt.3 12732 12732.0Breast array 568-627 DEX0455_055.nt.3 12731 12731.0 Breast array 731-790DEX0455_055.nt.3 20541 20541.01 Ovarian array 835-894 DEX0455_056.nt.123444 23444.01 Ovarian array 2588-2647 DEX0455_056.nt.1 3161 3161.0 Lungarray 2547-2606 DEX0455_056.nt.1 3164 3164.0 Lung array 3317-3376DEX0455_056.nt.1 3160 3160.0 Lung array 2588-2647 DEX0455_056.nt.1 31653165.0 Lung array 3277-3336 DEX0455_056.nt.1 1583 1583.0 Lung array3277-3336 DEX0455_056.nt.1 18520 18520.02 Ovarian array 3317-3376DEX0455_056.nt.1 3143 3143.0 Lung array 3107-3166 DEX0455_056.nt.1 15821582.0 Lung array 3317-3376 DEX0455_056.nt.1 22734 22734.02 Ovarianarray 3317-3376 DEX0455_056.nt.1 2661 2661.0 Lung array 3523-3582DEX0455_056.nt.2 23444 23444.01 Ovarian array 2559-2618 DEX0455_056.nt.22661 2661.0 Lung array 3287-3346 DEX0455_056.nt.2 3161 3161.0 Lung array2518-2577 DEX0455_056.nt.2 1582 1582.0 Lung array 3081-3140DEX0455_056.nt.2 22734 22734.02 Ovarian array 3081-3140 DEX0455_056.nt.23160 3160.0 Lung array 2559-2618 DEX0455_056.nt.2 18520 18520.02 Ovarianarray 3081-3140 DEX0455_056.nt.2 3165 3165.0 Lung array 3041-3100DEX0455_056.nt.2 1583 1583.0 Lung array 3041-3100 DEX0455_056.nt.2 31643164.0 Lung array 3081-3140 DEX0455_057.nt.1 7613 7613.0 Lung array292-351 DEX0455_057.nt.1 33332 33332.02 Prostate1 array 600-659DEX0455_057.nt.1 7612 7612.0 Lung array 381-440 DEX0455_057.nt.1 2452424524.02 Ovarian array 600-659 DEX0455_057.nt.2 7613 7613.0 Lung array458-517 DEX0455_057.nt.2 7612 1712.0 Lung array 547-606 DEX0455_057.nt.233332 33332.02 Prostate1 array 766-825 DEX0455_058.nt.1 14656 14656.02Ovarian array 555-614 DEX0455_059.nt.1 17372 17372.01 Ovarian array1778-1837 DEX0455_059.nt.1 11469 11469.02 Ovarian array 424-483DEX0455_059.nt.1 17370 17370.01 Ovarian array  957-1016 DEX0455_059.nt.217372 17372.01 Ovarian array 1489-1548 DEX0455_059.nt.2 11469 11469.02Ovarian array 424-483 DEX0455_060.nt.1 10372 10372.01 Ovarian array1201-1260 DEX0455_060.nt.1 18582 18582.01 Ovarian array 672-731DEX0455_061.nt.1 78508 78508.0 Multi-Cancer array 3736-3795DEX0455_061.nt.1 103529 103529.01 Ovarian array 3740-3799DEX0455_061.nt.1 19803 19803.0 Colon array 3736-3795 DEX0455_061.nt.196523 96523.02 Ovarian array 3740-3799 DEX0455_061.nt.1 19804 19804.0Colon array 3684-3743 DEX0455_061.nt.2 19803 19803.0 Colon array4690-4749 DEX0455_061.nt.2 78508 78508.0 Multi-cancer array 4690-4749DEX0455_061.nt.2 19804 19804.0 Colon array 4638-4697 DEX0455_061.nt.2103529 103529.01 Ovarian array 4694-4753 DEX0455_061.nt.2 96523 96523.02Ovarian array 4694-4753 DEX0455_061.nt.3 19803 19803.0 Colon array4556-4615 DEX0455_061.nt.3 78508 78508.0 Multi-Cancer array 4556-4615DEX0455_061.nt.3 103529 103529.01 Ovarian array 4560-4619DEX0455_061.nt.3 19804 19804.0 Colon array 4504-4563 DEX0455_061.nt.396523 96523.02 Ovarian array 4560-4619 DEX0455_061.nt.4 103529 103529.01Ovarian array 1702-1761 DEX0455_061.nt.4 19804 19804.0 Colon array1646-1705 DEX0455_061.nt.4 78508 78508.0 Multi-Cancer array 1698-1757DEX0455_061.nt.4 19803 19803.0 Colon array 1698-1757 DEX0455_061.nt.496523 96523.02 Ovarian array 1702-1761 DEX0455_061.nt.5 78508 78508.0Multi-Cancer array 2394-2453 DEX0455_061.nt.5 103529 103529.01 Ovarianarray 2398-2457 DEX0455_061.nt.5 19803 19803.0 Colon array 2394-2453DEX0455_061.nt.5 19804 19804.0 Colon array 2342-2401 DEX0455_061.nt.596523 96523.02 Ovarian array 2398-2457 DEX0455_062.nt.1 18094 18094.01Ovarian array 914-973 DEX0455_062.nt.1 17464 17464.02 Ovarian array1167-1226

Example 2b Relative Quantitation of Gene Expression

Real-Time quantitative PCR with fluorescent Taqman® probes is aquantitation detection system utilizing the 5′-3′ nuclease activity ofTaq DNA polymerase. The method uses an internal fluorescentoligonucleotide probe (Taqman®) labeled with a 5′ reporter dye and adownstream, 3′ quencher dye. During PCR, the 5′-3′ nuclease activity ofTaq DNA polymerase releases the reporter, whose fluorescence can then bedetected by the laser detector of the Model 7700 Sequence DetectionSystem (PE Applied Biosystems, Foster City, Calif., USA). Amplificationof an endogenous control is used to standardize the amount of sample RNAadded to the reaction and normalize for Reverse Transcriptase (RT)efficiency. Either cyclophilin, glyceraldehyde-3-phosphate dehydrogenase(GAPDH), ATPase, or 18S ribosomal RNA (rRNA) is used as this endogenouscontrol. To calculate relative quantitation between all the samplesstudied, the target RNA levels for one sample were used as the basis forcomparative results (calibrator). Quantitation relative to the“calibrator” can be obtained using the comparative method (User Bulletin#2: ABI PRISM 7700 Sequence Detection System).

The tissue distribution and the level of the target gene are evaluatedfor every sample in normal and cancer tissues. Total RNA is extractedfrom normal tissues, cancer tissues, and from cancers and thecorresponding matched adjacent tissues. Subsequently, first strand cDNAis prepared with reverse transcriptase and the polymerase chain reactionis done using primers and Taqman® probes specific to each target gene.The results are analyzed using the ABI PRISM 7700 Sequence Detector. Theabsolute numbers are relative levels of expression of the target gene ina particular tissue compared to the calibrator tissue.

One of ordinary skill can design appropriate primers. The relativelevels of expression of the OSNA versus normal tissues and other cancertissues can then be determined. All the values are compared to thecalibrator. Normal RNA samples are commercially available pools,originated by pooling samples of a particular tissue from differentindividuals.

The relative levels of expression of the OSNA in pairs of matchedsamples may also be determined. A matched pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. All thevalues are compared to the calibrator.

In the analysis of matching samples, the OSNAs show a high degree oftissue specificity for the tissue of interest. These results confirm thetissue specificity results obtained with normal pooled samples. Further,the level of mRNA expression in cancer samples and the isogenic normaladjacent tissue from the same individual are compared. This comparisonprovides an indication of specificity for the cancer state (e.g. higherlevels of mRNA expression in the cancer sample compared to the normaladjacent).

Information on the samples tested in the QPCR experiments below includethe Sample ID (Smpl ID), Organ, Tissue Type (Tiss Type), Diagnosis(DIAG), Disease Detail, and Stage or Grade (STG or GRD) in followingtable. Sample TISS STAGE OR ID ORGAN TYPE DIAGNOSIS DISEASE DETAIL GRADEA084 Ovary CAN Mucinous borderline tumor A084 Ovary NAT NAT G010 OvaryCAN Adenocarcinoma Adenocarcinoma Stage III G010 Ovary NAT NAT G021Ovary CAN Carcinoma St. IIIC, poorly Stage- diff. IIIC, poorly diff.G021 Ovary NAT NAT 1157 Ovary CAN malignant tumor 773O Ovary CANPapillary serous papillary metastatic adenocarcinoma adenocarcinoma 814OOvary CAN Papillary Serous Stage IV Adenocarcinoma C360 Ovary CANAdenocarcinoma endometrioid adenocarcinoma 1005O Ovary CAN papillaryserous 3 and endometrioid ovarian carcinoma, concurrent metastaticbreast cancer 1040O Ovary CAN papillary serous adeno, metastatic 105OOvary CAN Papillary Serous Stage IC Carcinoma with G0; Focal MucinousT1cN0M0 Differentiation 130X Ovary CAN Ovarian cancer 718O Ovary CANAdenocarcinoma malignant tumor IIIC A1B Ovary CAN Adenocarcinoma CA 988ZOvary CAN papillary serous poorly adenocarcinoma diff, FIGO IIIC 451OOvary NRM Normal Tissue 247A Ovary NRM NL 35GA Ovary NRM NL C087 OvaryNRM NL C109 Ovary NRM NL 206I Ovary NRM NL 515O Ovary NRM Normal 18GAOvary NRM NL 337O Ovary NRM Normal 123O Ovary NRM Normal C177 Ovary NRMseveral fluid filled cysts 40G Ovary NRM NL C004 Ovary NRM NL 030BUrinary CAN Carcinoma invasive Stage III, Bladder Carcinoma, poorlyGrade 3 differentiated 030B Urinary NAT NAT Bladder TR17 Urinary CANCarcinoma transitional StageII/GradeIII Bladder cell carcinoma TR17Urinary NAT NAT Bladder 520B Urinary CAN Sarcomatoid Sarcomatoid Bladdertransitional transitional cell carcinoma cell carcinoma 520B Urinary NATNAT Bladder 401C Colon CAN Adenocarcinoma Adenocarcinoma Stage III ofascending colon and cecum 401C Colon NAT NAT AS43 Colon CANAdenocarcinoma malignant AS43 Colon NAT Adenocarcinoma NAT AS98 ColonCAN Adenocarcinoma Moderately to Duke's C poorly differentiatedadenocarcinoma AS98 Colon NAT NAT CM12 Colon CAN T Stage D CM12 ColonNAT Adenocarcinoma Nat DC19 Colon CAN T Stage B DC19 Colon NAT NL RC01Colon CAN Cancer Stage IV RC01 Colon NAT NAT RS53 Colon CANAdenocarcinoma moderately differentiated adenocarcinoma RS53 Colon NATAdenocarcinoma NAT SG27 Colon CAN malig Stage B SG27 Colon NAT NAT TX01Colon CAN Adenocarcinoma Moderately Stage II; differentiated T3NoMoadenocarcinoma of cecum TX01 Colon NAT NAT KS52 Cervix CAN Squamous cellKeratinizing IIIB, well carcinoma Squamous Cell diff. G1; CarcinomaT3bNxM0 KS52 Cervix NAT NAT NK23 Cervix CAN Nonkeratinizing FIGO IIIB,Large Cell undiff. G4; T3bNxM0 NK23 Cervix NAT NAT NKS54 Cervix CANSquamous cell Nonkeratinizing IIB, mod carcinoma Squamous Cell diff. G2;Carcinoma T2bNxM0 NKS54 Cervix NAT NAT NKS55 Cervix CAN Squamous cellNonkeratinizing IIIB, Mod carcinoma Squamous Cell diff. G2; CarcinomaT3bNxM0 NKS55 Cervix NAT NAT NKS81 Cervix CAN Squamous cell large cellIIB carcinoma nonkeratinizing sq carc, IIB, moderately diff NKS81 CervixNAT NAT NKS25 Cervix CAN NKS25 Cervix NAT NAT NKS18 Cervix CAN Squamouscell Nonkeratinizing GII carcinoma squamous cell carcinoma NKS18 CervixNAT NAT 10479 Endometrium CAN malignant mixed T?, Nx, M1 mullerian tumor10479 Endometrium NAT NAT 28XA Endometrium CAN Endometrial malignantII/III adenocarcinoma 28XA Endometrium NAT NAT II/III 8XA EndometriumCAN mod. diff, invasive, squamous differentiation, FIGO-II 8XAEndometrium NAT NAT 106XD Kidney CAN Renal cell renal cell 3 carcinomacarcinoma, clear cell, localized 106XD Kidney NAT NL 107XD Kidney CANRenal cell renal cell G III carcinoma carcinoma, clear cell, withmetastatic 107XD Kidney NAT NL 109XD Kidney CAN Malignant G III 109XDKidney NAT NL 10XD Kidney CAN Renal cell renal cell 3 carcinomacarcinoma, clear cell, localized, grade 2-3 10XD Kidney NAT NL 22KKidney CAN Renal cell Renal cell G2, Mod. carcinoma carcinoma Diff. 22KKidney NAT NAT 12XD Kidney CAN Renal cell Left renal cell carcinomacarcinoma 12XD Kidney NAT NAT 15XA Liver CAN Sarcoma, RetroperitonealGrade-2 Tumor 15XA Liver NAT CA St. I, G4 174L Liver CAN HepatocellularModerate to well carcinoma differentiated hepatocellular carcinoma 174LLiver NAT Hepatocellular NAT carcinoma 187L Liver CAN AdenocarcinomaMetastatic Liver Adenocarcinoma (Gallbladder) 187L Liver NAT NAT 205LLung CAN Adenocarcinoma poorly T2, N1, Mx differentiated adenocarcinoma205L Lung NAT NAT 315L Lung CAN Squamous cell carcinoma 315L Lung NATAdenocarcinoma NAT 507L Lung CAN Bronchioloalveolar bronchioalveolarStage IB, carcinoma carcinoma G1, well diff. 507L Lung NAT NAT 528L LungCAN Adenocarcinoma Adenocarcinoma St.IV, T2N0 M1, infiltrating poorlydiff. 528L Lung NAT NAT 8837L Lung CAN Squamous cell Squamous cell T2,N0, M0 carcinoma carcinoma 8837L Lung NAT NAT AC11 Lung CANAdenocarcinoma poorly T2, N2, M1 differentiated adenocarcinoma AC11 LungNAT NAT AC39 Lung CAN Adenocarcinoma intermediate T2, N2, Mx gradeadnocarcinoma AC39 Lung NAT NAT SQ80 Lung CAN Squamous cell poorly T1,N1, M0 carcinoma differentiated squamous cell carcinoma SQ80 Lung NATNAT SQ81 Lung CAN Squamous cell poorly T3, N1, Mx carcinomadifferentiated squamous carcinoma SQ81 Lung NAT NAT 19DN Mammary CANInvasive ductal Invasive ductal G3, Stage carcinoma carcinoma IIA;T2N0M0 19DN Mammary NAT NAT 42DN Mammary CAN Invasive ductal InvasiveDuctal T3aN1M0 carcinoma Carcinoma IIIA, G3 42DN Mammary NAT NAT 517Mammary CAN Infiltrating Infiltrating St. IIA, ductal carcinoma ductalcarcinoma G3 517 Mammary NAT NAT 781M Mammary CAN Invasive ductalArchitectural carcinoma grade- 3/3, Nuclear grade- 3/3 781M Mammary NATNAT 869M Mammary CAN Invasive Invasive Stage IIA carcinoma Carcinoma G1;T2NoMo 869M Mammary NAT NAT 976M Mammary CAN Invasive ductal InvasiveDuctal T2N1M0 carcinoma Carcinoma (Stage 2B Grade 2-3) 976M Mammary NATNAT S570 Mammary CAN Carcinoma Carcinoma Stage IIA; T1N1Mo S570 MammaryNAT NAT S699 Mammary CAN Invasive lobular Invasive Lobular Stage IIBcarcinoma Carcinoma G1; T2N1Mo S699 Mammary NAT NAT S997 Mammary CANInvasive ductal Invasive Ductal Stage IIB carcinoma Carcinoma G3; T2N1MoS997 Mammary NAT NAT 71XL Pancreas CAN villous adenoma localized withpaneth cell metaplasia 71XL Pancreas NAT NL 82XP Pancreas CAN seriouscystadenoma 82XP Pancreas NAT NL 92X Pancreas CAN Ductal ductal mod toadenocarcinoma adenocarcinoma focally poorly diff. 92X Pancreas NAT NL77X Pancreas CAN Hepatic adenoma Hepatic adenoma 77X Pancreas NAT NL 23BProstate CAN Prostate tumor Gleason's 3 + 4 23B Prostate NAT NAT 65XBProstate CAN Adenocarcinoma adenocarcinom 3 + 4 = 7 65XB Prostate NAT NL675P Prostate CAN Adenocarcinoma adenocarcinoma 675P Prostate NAT Normal84XB Prostate CAN Adenocarcinoma adenocarcinom 2 + 3 84XB Prostate NATNL 958P Prostate CAN Adenocarcinoma Adenocarcinoma T2C, NO, MX 958PProstate NAT NAT Normal 263C Prostate BPH BPH 276P Prostate BPH BPH 767BProstate BPH prostate BPH 855P Prostate BPH BPH 10R Prostate PROSTactive chronic T0, N0, M0 prostatitis 20R Prostate PROST PROSTATITIS287S Skin CAN Squamous cell Invasive Moderately carcinoma KeratinizingDifferentiated Squamous Cell Carcinoma 287S Skin NAT NAT 39A Skin CAN CASt. II 39A Skin NAT CA St. II 669S Skin CAN Melanoma Nodular malignantmelanoma 669S Skin NAT NAT 171S Small CAN Adenocarcinoma ModeratelyIntestine differentiated Adenocarcinoma, invasive 171S Small NAT NATIntestine 20SM Small CAN Adenocarcinoma Adenocarcinoma, St. IV,Intestine metastic to lung poorly & liver diff. 20SM Small NAT NATIntestine H89 Small CAN Adenocarcinoma Adenocarcinoma 80% tumor,Intestine 50% necrosis, moderately differentiated, G2- 3; T3N1MX H89Small NAT Adenocarcinoma NAT Intestine 261S Stomach CAN Signet-ring cellSignet-ring cell Stage carcinoma carcinoma IIIA, T3N1M0 261S Stomach NATNAT 288S Stomach CAN Adenocarcinoma Infiltrating ModeratelyAdneocarcinoma Differentiated 288S Stomach NAT NAT AC93 Stomach CANAdenocarcinoma Adenocarcinoma St. IV, or G4, 509L T4N3M0, poorly diff.AC93 Stomach NAT NAT or 509L 88S Stomach CAN Adenocarcinoma MucinousT3N1M0, adenocarcinoma St. IIIA 88S Stomach NAT NAT 143N Thyroid CANFollicular Follicular Gland carcinoma Carcinoma 143N Thyroid NAT NATGland 270T Thyroid CAN CA Gland 270T Thyroid NAT NAT Gland 56T ThyroidCAN Papillary Papillary St. III; Gland carcinoma Carcinoma T4N1M0 56TThyroid NAT NAT Gland 39X Testes CAN CA 39X Testes NAT NAT 647T TestesCAN Teratocarcinoma Teratocarcinoma Stage IA 647T Testes NATTeratocarcinoma NAT 663T Testes CAN Teratocarcinoma Teratocarcinoma 663TTestes NAT NAT 135XO Uterus CAN Uterus normal 135XO Uterus NAT Uterustumor 85XU Uterus CAN endometrial I carcinoma 85XU Uterus NAT NL B1Blood NRM Normal B3 Blood NRM Normal B5 Blood NRM Normal B6 Blood NRMNormal B11 Blood NRM Normal 982B Blood NRM Normal B69 Blood NRM NormalB72 Blood NRM Normal B73 Blood NRM Normal B75 Blood NRM Normal 48ADAdrenal NRM Normal Gland 10BR Brain NRM Normal 01CL Colon NRM Normal06CV Cervix NRM Normal 01ES Esophagus NRM Normal 46HR Heart NRM Normal00HR Human CAN CAN Cancer pool Reference 55KD Kidney NRM Normal 89LVLiver NRM Normal 90LN Lung NRM Normal 01MA Mammary NRM Normal 84MUSkeletal NRM Normal Muscle 3APV Ovary NRM Normal 04PA Pancreas NRMNormal 59PL Placenta NRM Normal 09PR Prostate NRM Normal 21RC Rectum NRMNormal 59SM Small NRM Normal Intestine 7GSP Spleen NRM Normal 09STStomach NRM Normal 4GTS Testes NRM Normal 99TM Thymus NRM Normal Gland16TR Trachea NRM Normal 57UT Uterus NRM NormalDEX0455_(—)019.nt.1 (Ovr224)

The relative expression level of Ovr224 in various tissue samples isincluded below. Tissue samples include 68 pairs of matching samples, 10non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 4 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toovarian cancer sample OVR7730 (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.01 0.00 OVRG010 0.00 0.06 OVRG021 0.03 0.03 OVR1157 0.36OVR773O 1.00 OVR814O 0.02 OVRC360 0.02 OVR1005O 0.35 OVR1040O 0.10OVR105O 0.00 OVR130X 0.44 OVR718O 0.02 OVRA1B 0.04 OVR247A 0.00 OVR35GA0.00 OVRC087 0.00 OVRC109 0.00 OVR206I 0.00 OVR515O 0.00 OVR18GA 0.00OVR337O 0.00 OVR123O 0.00 OVRC177 0.02 OVR40G 0.00 OVRC004 0.00 BLD030B0.00 0.00 BLDTR17 0.00 0.03 CLN401C 0.00 0.00 CLNAS98 0.02 0.00 CLNCM120.00 0.02 CLNDC19 0.02 0.00 CLNRC01 0.00 0.01 CLNRS53 0.14 0.00 CLNSG270.00 0.00 CLNTX01 0.00 0.00 CVXKS52 0.00 0.03 CVXNK23 0.01 0.00 CVXNKS540.00 0.25 CVXNKS55 0.06 0.17 CVXNKS81 0.87 0.00 ENDO10479 0.03 0.00ENDO28XA 0.00 0.00 ENDO8XA 0.02 0.00 KID106XD 0.00 0.08 KID107XD 0.000.07 KID109XD 0.06 0.37 KID10XD 0.00 0.02 KID22K 0.00 0.00 LNG205L 0.000.33 LNG315L 0.00 0.53 LNG507L 0.21 0.43 LNG528L 0.00 2.39 LNG8837L 0.020.13 LNGAC11 0.32 0.23 LNGSQ80 0.00 0.00 LVR187L 0.00 0.04 MAM19DN 0.000.00 MAM42DN 0.13 0.00 MAM517 0.62 0.00 MAM781M 0.00 0.00 MAM869M 0.000.42 MAM976M 0.00 0.00 MAMS570 0.00 0.00 MAMS699 0.00 0.00 MAMS997 0.000.00 PAN71XL 0.01 0.04 PAN82XP 0.01 0.00 PAN92X 0.00 0.00 PRO23B 0.020.03 PRO65XB 0.01 0.02 PRO675P 0.07 0.00 PRO84XB 0.02 0.09 PRO958P 0.000.04 PRO263C 0.00 PRO276P 0.00 PRO767B 0.04 PRO855P 0.00 PRO10R 0.00PRO20R 0.00 SKN287S 0.00 0.00 SKN39A 0.62 0.73 SKN669S 0.02 0.00SMINT171S 0.00 0.00 SMINT20SM 0.04 0.00 SMINTH89 0.01 0.00 STO261S 0.000.00 STO288S 0.00 0.03 STO88S 0.04 0.03 THRD143N 0.00 0.04 THRD270T 0.050.03 THRD56T 0.44 0.05 TST39X 0.00 0.33 TST647T 0.02 0.07 TST663T 0.050.01 UTR135XO 0.05 0.00 UTR85XU 0.03 0.00 BLOB1 9.03 BLOB3 0.71 BLOB65.37 BLOB11 3.85 BLO982B 0.93 ADR48AD 0.00 BRN10BR 0.00 CLN01CL 0.00ESO01ES 0.22 HRT46HR 0.00 HUMREF00HR 0.00 KID55KD 0.03 LVR89LV 0.00LNG90LN 0.01 MAM01MA 0.00 MSL84MU 0.00 OVR3APV 0.01 PAN04PA 0.00 PLA59PL0.00 PRO09PR 0.00 REC21RC 0.00 SMINT59SM 0.01 SPL7GSP 0.63 STO09ST 0.00THYM99TM 0.00 TRA16TR 0.00 TST4GTS 0.03 UTR57UT 0.00Note:0.00 = Negative or Not Detected

The sensitivity for Ovr224 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr224 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr224 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up 44% 0% 22% 0% 20% vs. NAT Sensitivity, Down22% 56% 11% 0% 40% vs. NAT Sensitivity, Up 44% 33% 22% 92% 80% vs. NRMSensitivity, Down  0% 44%  0% 0%  0% vs. NRM Specificity 47.03%  54.59%   45.41%   56% 52.41%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr224 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr224 are as follows:(Ovr224_forward): TCCTCAAGGGCCCTCCCCAG (SEQ ID NO:296) (Ovr224_reverse):CCACAGCCATCTCCTCCATATTCTG (SEQ ID NO:297) (Ovr224_probe):AAGTGTTCCTCTGGATGACCTACCTGG (SEQ ID NO:298)DEX0455_(—)031.nt.2 (Cln252)

The relative expression level of Cln257 in various tissue samples isincluded below. Tissue samples include 78 pairs of matching samples, 6non matched cancer samples, and 35 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal colon sample CLN01CL (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST CLNAS12 5.55 10.39 CLNAS46 6.28 3.22 CLNB34 1.78 3.88 CLNC9XR 2.763.35 CLNCM67 2.91 2.44 CLNTX89 6.56 5.08 CLNAS43 27.92 6.39 CLNAS98 6.935.42 CLNRS53 8.04 6.77 CLNRC01 9.91 2.51 CLNSG27 4.56 7.39 CLNDC19 3.973.84 CLN401C 7.09 4.98 CLNCM12 3.28 6.25 CLNTX01 16.34 8.61 BLD030B 2.292.59 BLD520B 12.82 14.74 BLDTR17 10.50 5.28 CVXKS52 12.36 17.89 CVXNK2312.42 62.77 CVXNKS54 24.16 13.33 CVXNKS55 15.58 17.45 CVXNKS81 84.82132.51 ENDO10479 15.86 25.40 ENDO28XA 12.96 13.04 ENDO8XA 12.25 3.60KID106XD 0.32 1.89 KID107XD 29.14 4.27 KID109XD 8.21 5.31 KID10XD 5.610.84 KID22K 2.84 1.47 LNG205L 8.83 9.05 LNG315L 16.63 28.85 LNG507L13.87 27.96 LNG528L 20.05 27.89 LNG8837L 16.21 10.02 LNGAC11 15.21 14.83LNGAC39 49.00 16.41 LNGSQ80 18.40 11.35 LNGSQ81 7.80 54.12 LVR15XA 9.042.93 LVR174L 4.08 6.13 LVR187L 3.52 3.60 MAM19DN 14.68 14.78 MAM42DN12.41 26.01 MAM517 133.69 12.41 MAM781M 23.89 12.22 MAM869M 7.84 17.28MAM976M 39.22 32.92 MAMS570 21.06 26.04 MAMS699 6.70 0.00 MAMS997 11.3713.47 OVRG021 9.65 18.53 OVR1005O 36.75 OVR1040O 14.88 OVR105O 8.82OVR130X 32.30 OVR718O 22.87 OVRA1B 15.50 OVR123O 16.94 OVR18GA 13.92OVR206I 15.98 OVR337O 13.28 OVR40G 20.23 OVR515O 26.97 OVRC004 54.21OVRC177 6.97 PAN71XL 9.65 8.64 PAN82XP 7.20 24.22 PAN92X 8.74 26.55PRO23B 13.10 14.00 PRO65XB 6.20 10.57 PRO675P 20.64 27.15 PRO84XB 10.4610.35 PRO958P 11.48 10.47 PRO263C 35.87 PRO276P 7.20 PRO767B 17.09PRO855P 8.27 PRO10R 16.92 PRO20R 15.27 SKN287S 8.51 9.87 SKN39A 12.758.64 SKN669S 8.95 23.59 SMINT171S 9.57 15.19 SMINT20SM 30.83 12.12SMINTH89 10.91 10.48 STO261S 16.09 3.67 STO288S 8.76 3.43 STO88S 14.774.27 THRD143N 6.43 17.06 THRD270T 25.28 27.05 THRD56T 12.28 9.55 TST39X7.03 1.37 TST647T 4.87 5.35 TST663T 10.23 3.49 UTR135XO 10.47 13.31UTR85XU 25.28 27.08 BLOB1 82.99 BLOB3 15.84 BLOB6 81.31 BLOB11 12.68BLO982B 3.82 ADR48AD 1.96 HUMREF00HR 0.94 BRN10BR 0.00 CLN01CL 1.00ESO01ES 4.70 HRT46HR 0.59 KID55KD 0.58 LVR89LV 1.93 LNG90LN 3.14 MAM01MA6.01 MSL84MU 0.21 OVR3APV 5.62 PAN04PA 3.59 PLA59PL 5.14 PRO09PR 3.40REC21RC 8.88 SMINT59SM 3.09 SPL7GSP 3.91 STO09ST 2.19 THYM99TM 4.39TRA16TR 6.32 TST4GTS 1.10 UTR57UT 14.360.00 = Negative or Not Detected

The sensitivity for Cln257 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Cln257 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient

This specificity is an indication of the level of colon tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Cln257 beinguseful as an colon cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up 13% 11% 22% 0% 0% vs. NAT Sensitivity, Down 7% 22% 22% 0% 0% vs. NAT Sensitivity, Up 93% 100%  67% 29%  80%  vs.NRM Sensitivity, Down  0%  0%  0% 0% 0% vs. NRM Specificity 3.47%  6.49%   5.95%   6.42%   5.35%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Cln257 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingcolon cancer. Primers used for QPCR Expression Analysis of Cln257 are asfollows: (Cln257_forward): CTGAAGCCGAGCTCAAAGGT (SEQ ID NO:299)(Cln257_reverse): CCCTGCTCCCACTTGAGATC (SEQ ID NO:300) (Cln257_probe):TGTGAAAAGGAGGCTGGGTGCCAG (SEQ ID NO:301)DEX0455_(—)034.nt.1 and DEX0455_(—)034.nt.2 (Ovr223)

The relative expression level of Ovr223 in various tissue samples isincluded below. Tissue samples include 75 pairs of matching samples, 11non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 4 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toovarian cancer sample OVR7730 (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.12 0.05 OVRG010 0.04 0.24 OVRG021 0.16 0.05 OVR1157 0.32OVR773O 1.00 OVR814O 0.06 OVRC360 0.00 OVR1005O 0.75 OVR1040O 0.97OVR105O 0.80 OVR130X 2.15 OVR718O 0.80 OVRA1B 1.90 OVR247A 0.00 OVR35GA0.03 OVRC087 0.06 OVRC109 0.04 OVR206I 0.00 OVR515O 0.00 OVR18GA 0.12OVR337O 0.00 OVR123O 0.00 OVRC177 0.03 OVR40G 0.02 OVRC004 0.00 BLD030B0.00 0.00 BLD520B 0.74 0.02 BLDTR17 0.00 0.11 CLN401C 0.40 0.35 CLNAS431.05 0.16 CLNAS98 0.16 0.25 CLNCM12 0.21 0.31 CLNDC19 0.47 0.17 CLNRC010.31 0.31 CLNRS53 0.18 1.03 CLNSG27 0.00 0.29 CLNTX01 0.36 0.25 CVXKS520.00 0.74 CVXNK23 0.68 2.29 CVXNKS54 1.18 2.21 CVXNKS55 0.92 0.82CVXNKS81 1.72 ENDO10479 0.48 1.16 ENDO28XA 1.17 0.25 ENDO8XA 0.52 0.13KID106XD 0.05 0.05 KID107XD 0.00 0.21 KID109XD 0.14 0.61 KID10XD 0.000.06 KID22K 0.21 0.10 LNG205L 0.23 0.00 LNG315L 0.15 2.19 LNG507L 0.370.82 LNG528L 2.95 0.60 LNG8837L 0.45 0.70 LNGAC11 0.17 0.54 LNGAC39 1.860.23 LNGSQ80 0.82 0.00 LNGSQ81 1.06 0.69 LVR174L 0.00 0.00 LVR187L 0.000.29 MAM19DN 1.16 0.87 MAM42DN 0.60 0.00 MAM517 7.70 0.00 MAM781M 0.410.74 MAM869M 0.58 0.00 MAM976M 1.01 0.42 MAMS570 2.29 4.07 MAMS699 0.390.00 MAMS997 1.33 0.86 PAN71XL 0.44 0.77 PAN82XP 0.10 7.85 PAN92X 0.490.81 PRO23B 0.15 0.19 PRO65XB 0.20 0.52 PRO675P 0.43 0.32 PRO84XB 0.430.45 PRO958P 0.46 0.52 PRO263C 0.00 PRO276P 0.13 PRO767B 0.48 PRO855P0.28 PRO10R 0.34 PRO20R 0.95 SKN287S 0.49 0.46 SKN39A 0.00 0.16 SKN669S0.38 2.09 SMINT171S 0.70 0.51 SMINT20SM 0.83 0.31 SMINTH89 0.43 1.27STO261S 1.61 0.52 STO288S 0.39 0.16 STO88S 0.00 0.18 THRD143N 0.25 0.45THRD270T 0.95 2.10 THRD56T 2.62 0.23 TST39X 0.47 0.90 TST647T 0.38 0.16TST663T 0.30 0.02 UTR135XO 0.09 0.30 UTR85XU 1.07 0.59 BLOB1 0.00 BLOB60.00 BLOB11 0.95 BLO982B 0.00 ADR48AD 0.00 BRN10BR 0.00 CLN01CL 0.04CVX1ACV 7.20 ESO01ES 0.56 HRT46HR 0.00 HUMREF00HR 0.00 KID55KD 0.01LVR89LV 0.00 LNG90LN 0.26 MAM01MA 0.10 MSL84MU 0.00 OVR3APV 0.03 PAN04PA0.11 PLA59PL 0.33 PRO09PR 0.27 REC21RC 0.18 SMINT59SM 0.09 SPL7GSP 0.06STO09ST 0.21 THYM99TM 0.00 TRA16TR 0.69 TST4GTS 0.00 UTR57UT 0.140.00 = Negative or Not Detected

The sensitivity for Ovr223 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr223 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr223 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 22% 44% 56%  0% 0% Sensitivity, Downvs. 22% 33% 0% 0% 20%  NAT Sensitivity, Up vs. NRM 89% 44% 100%  85%  0%Sensitivity, Down vs. 11%  0% 0% 8% 0% NRM Specificity 24.32%   25.41%  30.81%    22.86%    25.67%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr223 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Additionally, the tissue specificity, plus the mRNA differentialexpression in the samples tested may make Ovr223 a good marker fordiagnosing, monitoring, staging, imaging and/or treating breast cancer.

Primers used for QPCR Expression Analysis of Ovr223 are as follows:(Ovr223_forward): AGTGAGAGGGTGGGCATGTATG (SEQ ID NO:302)(Ovr223_reverse): TACTCCAGGCGCTCTGAGGAT (SEQ ID NO:303) (Ovr223_probe):TTAGCCAGTGGCCTCCACTCTGTCCC (SEQ ID NO:304)DEX0455_(—)034.nt.4 (Ovr223v2)

The relative expression level of Ovr223v2 in various tissue samples isincluded below. Tissue samples include 74 pairs of matching samples, 11non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 4 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal pancreas sample PAN04PA (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.25 0.00 OVRG010 4.93 OVRG021 0.40 0.06 OVR1157 3.69OVR773O 7.06 OVR988Z 1.93 OVRC360 0.34 OVR1005O 2.85 OVR1040O 3.20OVR105O 3.02 OVR130X 1.84 OVR718O 2.15 OVRA1B 7.99 OVR247A 0.44 OVR35GA0.21 OVRC087 0.23 OVRC109 0.20 OVR206I 0.11 OVR515O 0.12 OVR18GA 0.07OVR337O 0.20 OVR123O 0.93 OVRC177 0.10 OVR40G 0.05 OVR451O 0.32 BLD030B0.20 1.10 BLD520B 2.00 0.18 BLDTR17 0.39 1.04 CLN401C 0.85 1.23 CLNAS432.68 0.16 CLNAS98 0.61 0.35 CLNCM12 0.61 0.80 CLNDC19 1.94 1.18 CLNRC010.46 0.42 CLNRS53 0.54 1.26 CLNSG27 0.61 0.65 CLNTX01 1.62 0.59 CVXKS523.54 4.98 CVXNKS55 7.35 4.40 CVXNKS25 4.23 4.81 CVXNKS18 1.26 3.88CVXNKS54 3.00 1.47 ENDO10479 3.07 0.37 ENDO28XA 4.24 0.69 ENDO8XA 0.313.57 KID106XD 0.11 0.33 KID12XD 0.27 2.13 KID10XD 0.10 0.21 KID22K 0.600.28 KID107XD 0.16 0.44 LNG205L 0.81 1.09 LNG315L 0.89 2.02 LNG507L 1.161.68 LNG528L 9.15 1.43 LNG8837L 1.46 1.65 LNGAC11 0.86 1.78 LNGAC39 6.931.66 LNGSQ80 1.13 0.32 LNGSQ81 1.95 1.13 LVR15XA 0.01 0.03 LVR174L 0.000.01 LVR187L 0.00 2.35 MAM19DN 3.52 3.45 MAM42DN 0.83 1.62 MAM517 10.393.02 MAM781M 1.80 0.34 MAM869M 1.85 0.13 MAM976M 4.08 0.67 MAMS570 2.434.41 MAMS699 1.16 1.50 MAMS997 1.20 1.39 PAN71XL 1.91 1.83 PAN77X 0.000.02 PAN92X 3.25 0.25 PRO10R 2.41 PRO20R 1.07 PRO23B 1.32 1.17 PRO263C1.30 PRO276P 0.88 PRO65XB 0.87 1.60 PRO675P 1.50 0.69 PRO767B 4.10PRO84XB 1.41 1.13 PRO855P 1.16 PRO958P 2.49 2.56 SKN287S 0.76 0.57SKN39A 0.25 0.20 SKN669S 0.60 1.12 SMINT171S 1.06 2.38 SMINT20SM 3.201.14 SMINTH89 1.92 1.80 STO261S 3.86 0.75 STO288S 1.00 0.23 STOAC93 0.662.01 STO88S 2.57 0.20 THRD143N 1.77 1.15 THRD270T 2.23 2.56 THRD56T 3.020.40 TST39X 0.80 0.77 TST647T 1.15 0.43 TST663T 0.55 0.05 UTR135XO 0.580.52 UTR85XU 2.70 1.49 BLOB3 0.19 BLOB11 0.93 BLO69 0.10 BLO72 0.06BLO73 0.13 ADR48AD 0.15 BRN10BR 0.00 CLN01CL 1.03 CVX06CV 0.48 ESO01ES3.34 HRT46HR 0.01 HUMREF00HR 0.08 KID55KD 0.27 LVR89LV 0.03 LNG90LN 3.99MAM01MA 2.38 MSL84MU 0.00 OVR3APV 0.13 PAN04PA 1.00 PRO09PR 3.27 REC21RC2.01 SMINT59SM 0.55 SPL7GSP 0.46 STO09ST 0.98 THYM99TM 0.54 TRA16TR 3.04TST4GTS 0.10 UTR57UT 0.430.00 = Negative or Not Detected

The sensitivity for Ovr223v2 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr223v2 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr223v2 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, 22% 33% 44% 0% 20% Up vs. NAT Sensitivity, 11%22%  0% 0%  0% Down vs. NAT Sensitivity, Up 11% 11% 11% 85%   0% vs. NRMSensitivity, 11% 78% 22% 0% 80% Down vs. NRM Specificity 8.06%   12.9%  16.67%   19.77%    14.89%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr223v2 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr223v2 are as follows:(Ovr223v2_forward): TCCAGATGGCTCAGCTTCTTC (SEQ ID NO:305)(Ovr223v2_reverse): GAAGGTGTTCGGAGAATGAGTGA (SEQ ID NO:306)(Ovr223v2_probe): TTTCTTCTGTGGCTCTGTGTTTTCCAGGC (SEQ ID NO:307)DEX0455_(—)037.nt.6 (Ovr229)

The relative expression level of Ovr229 in various tissue samples isincluded below. Tissue samples include 74 pairs of matching samples, 10non matched cancer samples, and 40 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal prostate sample PRO09PR (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.01 0.00 OVRG010 0.36 0.00 OVRG021 0.39 0.09 OVR1157 0.00OVR773O 0.31 OVR988Z 1.25 OVRC360 1.64 OVR1005O 0.47 OVR1040O 1.49OVR105O 0.33 OVR130X 0.00 OVR718O 0.42 OVRA1B 0.27 OVR247A 0.00 OVR35GA0.05 OVRC087 0.40 OVRC109 0.00 OVR206I 0.12 OVR515O 0.42 OVR18GA 0.00OVR337O 0.00 OVR123O 0.00 OVRC177 0.22 OVR40G 0.00 OVR451O 0.00 BLD030B0.04 0.14 BLD520B 0.00 0.23 BLDTR17 0.37 0.19 CLN401C 0.04 0.04 CLNAS430.10 0.14 CLNAS98 0.00 0.00 CLNCM12 0.11 0.12 CLNDC19 0.00 0.09 CLNRC010.01 0.02 CLNRS53 0.00 0.00 CLNSG27 0.08 0.31 CLNTX01 0.00 0.24 CVXKS520.00 0.35 CVXNKS55 0.03 0.25 CVXNKS25 1.68 0.25 CVXNKS18 0.00 0.06CVXNKS54 0.00 1.22 ENDO10479 0.13 0.35 ENDO28XA 0.18 0.54 ENDO8XA 0.000.05 KID106XD 0.00 0.02 KID12XD 0.01 0.37 KID10XD 0.00 0.01 KID22K 0.020.06 KID107XD 0.00 0.02 LNG205L 0.01 1.04 LNG315L 0.14 1.69 LNG507L 0.483.36 LNG528L 0.00 0.71 LNG8837L 0.12 1.08 LNGAC11 0.10 0.20 LNGAC39 0.522.65 LNGSQ80 0.16 2.29 LNGSQ81 0.23 2.01 LVR15XA 0.00 0.03 LVR174L 0.000.02 LVR187L 0.00 0.00 MAM19DN 0.00 0.28 MAM42DN 0.17 0.00 MAM517 2.590.00 MAM781M 0.00 0.00 MAM869M 0.05 0.74 MAM976M 0.26 0.00 MAMS570 0.000.00 MAMS699 0.28 0.89 MAMS997 0.13 0.23 PAN71XL 0.06 0.09 PAN77X 0.000.05 PAN92X 0.27 0.00 PRO10R 1.00 PRO20R 8.84 PRO23B 1.11 1.14 PRO263C1.16 PRO276P 0.93 PRO65XB 0.14 0.85 PRO675P 0.42 0.51 PRO767B 0.88PRO84XB 0.15 3.51 PRO855P 2.76 PRO958P 0.76 2.69 SKN287S 0.22 2.01SKN39A 0.16 0.00 SKN669S 0.40 0.00 SMINT171S 0.02 0.04 SMINT20SM 0.070.15 SMINTH89 0.05 0.00 STO261S 0.00 0.11 STO288S 0.02 0.12 STOAC93 0.230.05 THRD143N 0.00 0.27 THRD270T 0.09 0.07 THRD56T 0.00 0.00 TST39X 0.008.21 TST647T 0.19 9.27 TST663T 0.14 10.16 UTR135XO 0.58 0.35 UTR85XU0.00 0.09 BLOB3 0.00 BLOB11 0.00 BLO69 0.00 BLO72 0.17 BLO73 0.00ADR48AD 0.00 BRN10BR 2.25 CLN01CL 0.10 CVX06CV 2.46 ESO01ES 0.00 HRT46HR0.88 HUMREF00HR 0.00 KID55KD 0.02 LVR89LV 0.03 LNG90LN 0.03 MAM01MA 0.02MSL84MU 0.02 OVR3APV 0.08 PAN04PA 0.29 PLA59PL 1.46 PRO09PR 1.00 REC21RC0.67 SMINT59SM 0.04 SPL7GSP 0.80 STO09ST 0.10 THYM99TM 0.46 TRA16TR 0.15TST4GTS 12.18 UTR57UT 1.540.00 = Negative or Not Detected

The sensitivity for Ovr229 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr229 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr229 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT  0%  0% 33% 0%  0% Sensitivity, Downvs. 44% 100%  33% 0% 60% NAT Sensitivity, Up vs. NRM  0% 78% 67% 85%  0% Sensitivity, Down vs. 67% 22% 33% 0% 60% NRM Specificity 26.06%  31.38%   28.19%   35.96%    42.11%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr229 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr229 are as follows:(Ovr229_forward): CCTGCCGCGGAGATCCAT (SEQ ID NO:308) (Ovr229_reverse):GCAGCGCGTACTGGTCGTA (SEQ ID NO:309) (Ovr229_probe):CCTACTCCGTGTCAGTGGTGGAG (SEQ ID NO:310)DEX0455_(—)037.nt.7 (Ovr227)

The relative expression level of Ovr227 in various tissue samples isincluded below. Tissue samples include 74 pairs of matching samples, 10non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toprostate normal sample PRO09PR (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 1.31 0.24 OVRG010 1.65 0.75 OVRG021 0.87 0.00 OVR1157 0.85OVR773O 0.21 OVR814O 0.24 OVRC360 0.58 OVR1005O 0.33 OVR1040O 0.11OVR105O 0.12 OVR130X 0.15 OVR718O 0.32 OVRA1B 0.11 OVR247A 0.40 OVR35GA0.06 OVRC087 0.16 OVRC109 0.08 OVR206I 0.00 OVR515O 0.63 OVR18GA 0.00OVR337O 0.00 OVR123O 0.00 OVRC177 0.03 OVR40G 0.02 OVRC004 0.00 BLD030B0.02 0.00 BLD520B 0.00 0.06 BLDTR17 0.00 0.00 CLN401C 0.02 0.04 CLNAS430.00 0.00 CLNAS98 0.00 0.09 CLNCM12 0.06 0.05 CLNDC19 0.04 0.10 CLNRC010.00 0.00 CLNRS53 0.18 0.40 CLNSG27 0.00 0.28 CLNTX01 0.58 0.00 CVXKS520.00 0.49 CVXNK23 0.00 0.00 CVXNKS54 1.12 2.58 CVXNKS55 0.01 0.00CVXNKS81 0.00 0.00 ENDO10479 0.00 2.93 ENDO28XA 0.76 0.52 ENDO8XA 0.030.00 KID106XD 0.00 0.00 KID107XD 0.00 0.04 KID109XD 0.00 0.00 KID10XD0.21 0.02 KID22K 0.01 0.02 LNG205L 0.00 0.35 LNG315L 0.33 1.50 LNG507L0.24 2.81 LNG528L 0.00 0.42 LNG8837L 0.18 1.12 LNGAC11 0.20 0.04 LNGAC390.59 1.37 LNGSQ80 1.38 1.09 LNGSQ81 0.65 1.59 LVR15XA 0.00 0.02 LVR174L0.00 0.01 LVR187L 0.00 0.09 MAM19DN 0.00 0.07 MAM42DN 0.16 0.00 MAM5170.00 0.00 MAM781M 0.00 0.24 MAM869M 0.00 0.00 MAM976M 0.12 0.00 MAMS5700.00 0.00 MAMS699 0.53 0.00 MAMS997 0.20 0.11 PAN71XL 0.00 0.03 PAN82XP0.00 0.00 PAN92X 0.10 0.78 PRO23B 0.35 0.20 PRO65XB 0.05 0.61 PRO675P0.22 0.40 PRO84XB 0.12 1.68 PRO958P 0.18 0.31 PRO263C 0.32 PRO276P 0.21PRO767B 0.69 PRO855P 0.29 PRO10R 0.38 PRO20R 1.35 SKN287S 0.00 2.19SKN39A 0.17 0.00 SKN669S 0.14 0.12 SMINT171S 0.39 0.15 SMINT20SM 0.060.07 SMINTH89 0.01 0.00 STO261S 0.60 0.18 STO288S 0.03 0.04 STO88S 0.000.07 THRD143N 0.01 0.04 THRD270T 0.03 0.03 THRD56T 0.00 0.14 TST39X 0.001.74 TST647T 0.02 3.30 TST663T 0.05 0.68 UTR135XO 0.22 0.17 UTR85XU 0.120.19 BLOB1 7.89 BLOB3 0.00 BLOB6 0.00 BLOB11 0.07 BLO982B 2.25 ADR48AD0.00 BRN10BR 1.02 CLN01CL 0.00 ESO01ES 0.25 HRT46HR 0.10 HUMREF00HR 0.00KID55KD 0.01 LVR89LV 0.02 LNG90LN 0.11 MAM01MA 0.00 MSL84MU 0.07 OVR3APV0.02 PAN04PA 0.20 PLA59PL 0.42 PRO09PR 1.00 REC21RC 0.28 SMINT59SM 0.01SPL7GSP 1.33 STO09ST 0.02 THYM99TM 0.38 TRA16TR 0.10 TST4GTS 2.47UTR57UT 0.430.00 = Negative or Not Detected

The sensitivity for Ovr227 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr227 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr227 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGNAM OVR PRO Sensitivity, Up vs. NAT 11% 11% 33% 0% 0% Sensitivity, Downvs. 67% 78% 22% 0% 40%  NAT Sensitivity, Up vs. NRM 56% 56% 44% 100%  0%Sensitivity, Down vs.  0% 22%  0% 0% 100%  NRM Specificity 28.11%  40.54%   25.41%   42.86%    39.04%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr227 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr227 are as follows:(Ovr227_forward): AGAGGCGCCCCCGCAGGTA (SEQ ID NO:311) (Ovr227_reverse):CCCGGAGCCAGCTCGAGTT (SEQ ID NO:312) (Ovr227_probe):CAGGAACTGCGGCGAGCGACCC (SEQ ID NO:313)DEX0455_(—)040.nt.2 (Ovr218)

The relative expression level of Ovr218 in various tissue samples isincluded below. Tissue samples include 75 pairs of matching samples, 10non matched cancer samples, and 41 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 6 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tocancer pool reference HUMREF00HR (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.46 0.17 OVRG010 1.55 3.95 OVRG021 6.74 6.08 OVR1157 4.90OVR773O 8.80 OVR814O 3.90 OVRC360 1.37 OVR1005O 19.92 OVR1040O 20.35OVR105O 5.63 OVR130X 19.60 OVR718O 55.03 OVRA1B 34.34 OVR247A 1.35OVR35GA 2.50 OVRC087 0.98 OVRC109 0.23 OVR206I 3.37 OVR515O 1.42 OVR18GA1.49 OVR337O 3.54 OVR123O 3.29 OVRC177 3.49 OVR40G 1.62 OVRC004 9.36BLD030B 3.36 0.72 BLD520B 3.23 2.25 BLDTR17 1.08 1.89 CLN401C 3.90 3.01CLNAS43 4.55 1.92 CLNAS98 3.44 2.33 CLNCM12 3.07 3.22 CLNDC19 7.72 2.05CLNRC01 1.80 2.17 CLNRS53 2.59 3.02 CLNSG27 2.69 4.49 CLNTX01 5.68 5.10CVXKS52 9.10 10.59 CVXNK23 9.81 41.11 CVXNKS54 20.97 12.22 CVXNKS5537.01 21.89 CVXNKS81 17.75 35.18 ENDO10479 13.27 1.33 ENDO28XA 13.534.98 ENDO8XA 0.34 0.58 KID106XD 0.28 0.70 KID107XD 5.01 2.27 KID109XD7.16 4.83 KID10XD 1.34 0.46 KID22K 2.79 0.65 LNG205L 1.40 4.10 LNG315L8.68 8.32 LNG507L 6.50 4.85 LNG528L 9.26 4.03 LNG8837L 4.36 5.37 LNGAC112.50 4.70 LNGAC39 16.03 4.63 LNGSQ80 3.70 0.84 LNGSQ81 14.10 7.33LVR15XA 0.05 0.03 LVR174L 0.15 0.12 LVR187L 0.00 9.89 MAM19DN 17.3217.15 MAM42DN 15.00 9.52 MAM517 66.52 6.34 MAM781M 4.45 3.02 MAM869M9.21 1.73 MAM976M 28.64 3.82 MAMS570 22.00 25.62 MAMS699 5.42 5.54MAMS997 10.63 7.95 PAN71XL 5.56 5.74 PAN82XP 2.41 26.35 PAN92X 52.916.82 PRO23B 7.13 7.97 PRO65XB 5.61 6.99 PRO675P 7.00 4.30 PRO84XB 7.186.80 PRO958P 6.32 4.35 PRO263C 6.28 PRO276P 4.78 PRO767B 10.75 PRO855P5.51 PRO10R 9.97 PRO20R 8.32 SKN287S 6.30 6.42 SKN39A 4.04 1.83 SKN669S6.16 19.67 SMINT171S 11.57 8.96 SMINT20SM 10.72 4.23 SMINTH89 5.77 4.77STO261S 8.85 2.39 STO288S 2.33 1.18 STO509L 5.78 10.86 STO88S 4.07 1.01THRD143N 8.25 15.21 THRD270T 10.97 7.35 THRD56T 9.88 11.23 TST39X 9.414.59 TST647T 11.31 1.05 TST663T 7.35 2.94 UTR135XO 2.34 5.62 UTR85XU17.13 6.68 BLOB1 7.23 BLOB3 3.50 BLOB5 122.49 BLOB6 9.34 BLOB11 5.44BLO982B 14.78 ADR48AD 0.61 BRN10BR 0.99 CLN01CL 0.51 CVX1ACV 14.89ESO01ES 5.63 HRT46HR 0.00 HUMREF00HR 1.00 KID55KD 0.29 LVR89LV 0.05LNG90LN 2.25 MAM01MA 1.00 MSL84MU 0.00 OVR3APV 0.93 PAN04PA 2.42 PLA59PL3.63 PRO09PR 3.03 REC21RC 2.74 SMINT59SM 2.21 SPL7GSP 1.19 STO09ST 0.87THYM99TM 5.68 TRA16TR 8.67 TST4GTS 9.06 UTR57UT 1.930.00 = Negative or Not Detected

The sensitivity for Ovr218 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr218 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr218 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, 22%  33% 33%  0% 0% Up vs. NAT Sensitivity, 0%11% 0% 0% 0% Down vs. NAT Sensitivity, 100%  56% 100%  77%  80%  Up vs.NRM Sensitivity, 0%  0% 0% 8% 0% Down vs. NRM Specificity 6.88%  9.52%   20.63%    8.94%   9.95%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr218 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Additionally, the tissue specificity, plus the mRNA differentialexpression in the samples tested may make Ovr218 a good marker fordiagnosing, monitoring, staging, imaging and/or treating breast cancer.

Primers used for QPCR Expression Analysis of Ovr218 are as follows:(Ovr218_forward): TGCCCAGCTGTGGTTTACATTA (SEQ ID NO:314)(Ovr218_reverse): CACCACCTCGCCATTCTCA (SEQ ID NO:315) (Ovr218_probe):TTCACTGTGAACATCATCTTGGCA (SEQ ID NO:316)DEX0455_(—)049.nt.1 (Ovr232)

The relative expression level of Ovr232 in various tissue samples isincluded below. Tissue samples include 73 pairs of matching samples, 10.non matched cancer samples, and 36 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 4 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toovarian cancer sample OVRAO84 (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 1.00 0.10 OVRG010 0.01 0.31 OVRG021 0.39 0.02 OVR1157 2.79OVR773O 1.14 OVR814O 0.37 OVRC360 0.00 OVR1005O 5.91 OVR1040O 5.77OVR105O 1.68 OVR130X 1.08 OVR718O 0.55 OVRA1B 4.48 OVR247A 0.00 OVR35GA0.00 OVRC087 0.00 OVRC109 0.00 OVR206I 0.03 OVR515O 0.00 OVR18GA 0.00OVR123O 0.00 OVRC177 0.02 OVR40G 0.00 OVRC004 0.00 BLD030B 0.26 0.00BLD520B 0.13 0.02 BLDTR17 0.24 0.25 CLN401C 3.46 2.62 CLNAS43 4.08 1.49CLNAS98 1.19 5.27 CLNCM12 2.46 7.45 CLNDC19 9.09 1.85 CLNRC01 2.55 3.52CLNRS53 1.38 9.36 CLNSG27 4.28 3.65 CLNTX01 3.83 4.54 CVXKS52 0.15 0.12CVXNK23 0.13 0.00 CVXNKS54 0.59 0.54 CVXNKS55 0.58 0.15 CVXNKS81 0.250.61 ENDO10479 6.19 1.01 ENDO28XA 6.03 0.82 ENDO8XA 0.40 1.67 KID106XD0.02 0.24 KID107XD 0.10 0.34 KID109XD 0.07 0.59 KID10XD 0.00 0.15 KID22K0.05 0.14 LNG205L 0.08 1.91 LNG315L 1.42 0.43 LNG507L 0.96 0.87 LNG528L9.39 0.92 LNG8837L 1.08 0.45 LNGAC11 0.28 1.23 LNGAC39 13.19 0.76LNGSQ80 2.02 0.86 LNGSQ81 2.19 0.67 LVR15XA 0.00 0.01 LVR174L 0.00 0.01LVR187L 0.00 10.06 MAM19DN 0.46 0.85 MAM42DN 0.71 0.74 MAM517 3.27 0.33MAM781M 1.52 0.34 MAM976M 0.83 0.37 MAMS570 0.35 1.02 MAMS699 0.28 0.39MAMS997 1.23 0.52 PAN71XL 6.96 4.45 PAN82XP 0.15 2.74 PAN92X 2.89 0.00PRO23B 0.23 0.12 PRO65XB 0.24 0.50 PRO675P 0.40 0.21 PRO84XB 0.45 0.30PRO958P 0.22 0.21 PRO263C 0.27 PRO276P 0.12 PRO767B 0.24 PRO855P 0.21PRO10R 0.18 PRO20R 0.44 SKN287S 0.38 0.11 SKN39A 0.00 0.00 SKN669S 0.030.08 SMINT171S 3.18 4.30 SMINT20SM 8.08 5.63 SMINTH89 8.24 3.50 STO261S6.10 2.42 STO288S 5.52 0.23 STO88S 2.64 0.14 THRD143N 1.00 5.56 THRD270T8.64 11.30 THRD56T 3.91 1.96 TST39X 0.42 0.56 TST647T 4.38 0.11 TST663T2.81 0.13 UTR135XO 0.40 0.48 UTR85XU 3.06 1.79 BLOB3 0.31 BLOB6 0.00BLOB11 0.00 BLO982B 0.00 ADR48AD 0.00 BRN10BR 0.07 CLN01CL 0.57 ESO01ES0.00 HUMREF00HR 0.17 KID55KD 0.05 LVR89LV 0.00 LNG90LN 2.56 MAM01MA 0.13MSL84MU 0.00 OVR3APV 0.00 PAN04PA 0.09 PLA59PL 0.00 PRO09PR 0.30 REC21RC4.27 SMINT59SM 0.97 SPL7GSP 0.03 STO09ST 0.09 THYM99TM 0.04 TRA16TR 0.43TST4GTS 0.11 UTR57UT 0.070.00 = Negative or Not Detected

The sensitivity for Ovr232 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr232 at least 2 foldhigher than the normal tissue or the corresponding normal adjacent formthe same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr232 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 22% 67% 44% 0% 0% Sensitivity, Downvs. 33% 22% 11%  0% 20%  NAT Sensitivity, Up vs. NRM 100%  22% 100%  92%0% Sensitivity, Down vs.  0% 44%  0%  8% 0% NRM Specificity 50.82%  33.88%   22.95%   21.84%   19.46%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr232 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr232 are as follows:(Ovr232_forward): GCTCAAAGCGTGAGTAAAATATCCT (SEQ ID NO:317)(Ovr232_reverse): CCACACTTACTTTGTAACATGATTCAGA (SEQ ID NO:318)(Ovr232_probe): TTTGACTTAATACTTCTTTAATTGATGTGCCTTG (SEQ ID NO:319)AGTTGGDEX0455_(—)049.nt.2 (Ovr232v1)

The relative expression level of Ovr232v1 in various tissue samples isincluded below. Tissue samples include 75 pairs of matching samples, 10non matched cancer samples, and 40 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal colon sample CLN01CL (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.02 0.67 OVRG010 0.00 0.00 OVRG021 0.10 0.00 OVR1157 0.00OVR773O 0.00 OVR988Z 0.00 OVRC360 0.00 OVR1005O 0.42 OVR1040O 0.53OVR105O 0.09 OVR130X 0.53 OVR718O 0.25 OVRA1B 0.26 OVR247A 0.00 OVR35GA0.05 OVRC087 0.00 OVRC109 0.00 OVR206I 0.00 OVR515O 0.00 OVR18GA 0.00OVR337O 0.00 OVR123O 0.38 OVRC177 0.01 OVR40G 0.00 OVR451O 0.00 BLD030B0.06 0.09 BLD520B 0.20 0.03 BLDTR17 0.46 0.01 CLN401C 0.18 0.22 CLNAS430.39 0.21 CLNAS98 0.31 0.47 CLNCM12 0.10 0.20 CLNDC19 0.40 0.07 CLNRC010.27 0.13 CLNRS53 0.15 0.33 CLNSG27 0.17 0.25 CLNTX01 0.13 0.20 CVXKS520.00 0.00 CVXNKS55 0.00 0.12 CVXNKS25 0.85 0.00 CVXNKS18 0.00 0.00CVXNKS54 0.00 0.00 ENDO10479 0.13 0.00 ENDO28XA 0.32 0.12 ENDO8XA 0.070.40 KID106XD 0.05 0.10 KID12XD 0.04 0.12 KID10XD 0.05 0.05 KID22K 0.020.03 KID107XD 0.00 0.04 LNG205L 0.00 0.26 LNG315L 0.38 0.00 LNG507L 0.200.00 LNG528L 0.37 0.37 LNG8837L 0.10 0.06 LNGAC11 0.03 0.06 LNGAC39 0.580.63 LNGSQ80 0.21 0.19 LNGSQ81 0.15 0.00 LVR15XA 0.00 0.00 LVR174L 0.000.00 LVR187L 0.00 0.37 MAM19DN 0.12 0.25 MAM42DN 0.44 0.64 MAM517 0.250.00 MAM781M 0.24 0.67 MAM869M 0.04 0.00 MAM976M 0.22 0.00 MAMS570 0.000.47 MAMS699 0.00 0.00 MAMS997 0.11 0.04 PAN71XL 1.10 0.31 PAN77X 0.000.00 PAN92X 0.19 0.00 PRO10R 0.00 PRO20R 0.20 PRO23B 0.17 0.10 PRO263C0.54 PRO276P 0.27 PRO65XB 0.17 0.11 PRO675P 0.47 0.85 PRO767B 0.10PRO84XB 0.12 0.13 PRO855P 0.08 PRO958P 0.15 0.12 SKN287S 0.10 0.00SKN39A 0.06 0.00 SKN669S 0.00 0.51 SMINT171S 0.38 0.67 SMINT20SM 0.230.40 SMINTH89 0.14 0.31 STO261S 0.69 0.24 STO288S 0.36 0.17 STOAC93 0.000.00 STO88S 0.00 0.17 THRD143N 0.15 0.25 THRD270T 0.37 0.28 THRD56T 0.340.45 TST39X 0.20 0.43 TST647T 0.59 0.41 TST663T 0.33 0.25 UTR135XO 0.190.13 UTR85XU 1.42 0.14 BLOB3 0.00 BLOB11 0.00 BLO69 0.00 BLO72 0.00BLO73 0.00 ADR48AD 0.00 BRN10BR 0.00 CLN01CL 0.12 CVX06CV 0.00 ESO01ES0.00 HRT46HR 0.00 HUMREF00HR 0.08 KID55KD 0.02 LVR89LV 0.00 LNG90LN 1.00MAM01MA 0.10 MSL84MU 0.00 OVR3APV 0.03 PAN04PA 0.17 PLA59PL 0.00 PRO09PR0.00 REC21RC 0.36 SMINT59SM 0.13 SPL7GSP 0.09 STO09ST 0.39 THYM99TM 0.00TRA16TR 0.09 TST4GTS 0.50 UTR57UT 0.150.00 = Negative or Not Detected

The sensitivity for Ovr232v1 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr232v1 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr232v1 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 22% 33% 44% 0% 0% Sensitivity, Downvs. 22% 22% 33% 0% 0% NAT Sensitivity, Up vs. NRM 44%  0% 44% 62%  100% Sensitivity, Down vs.  0% 89% 33% 0% 0% NRM Specificity 36.7%   34.57%  32.45%   28.65%    35.26%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr232v1 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr232v1 are as follows:(Ovr232v1_forward): GGCGGTGACTCATCAACGA (SEQ ID NO:320)(Ovr232v1_reverse): CATTGACGATTATTATTCACAAAGCA (SEQ ID NO:321)(Ovr232v1_probe): GCGGCCAGAGAATGTGTCTGTGAAAACT (SEQ ID NO:322)DEX0455_(—)049.nt.3 (Ovr232v2)

The relative expression level of Ovr232v2 in various tissue samples isincluded below. Tissue samples include 72 pairs of matching samples, 12non matched cancer samples, and 37 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal spleen sample SPL7GSP (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 20.82 1.47 OVRG010 7.06 0.00 OVRG021 2.01 0.55 OVR115717.09 OVR773O 31.56 OVR988Z 17.68 OVRC360 0.00 OVR1005O 20.28 OVR1040O29.36 OVR105O 15.24 OVR130X 10.08 OVR718O 12.73 OVRA1B 34.60 OVR247A0.00 OVR35GA 0.11 OVRC087 0.00 OVRC109 0.00 OVR206I 0.43 OVR515O 1.11OVR18GA 0.00 OVR123O 3.47 OVRC177 0.08 OVR40G 0.06 BLD030B 6.81 0.00BLD520B 4.04 0.57 BLDTR17 3.89 2.17 CLN401C 22.89 17.80 CLNAS43 72.6516.04 CLNAS98 15.32 35.15 CLNCM12 17.48 29.75 CLNDC19 81.83 20.01CLNRC01 20.30 18.70 CLNRS53 17.98 55.34 CLNSG27 59.40 41.80 CLNTX0130.45 37.83 CVXKS52 3.47 2.77 CVXNKS55 12.43 2.43 CVXNKS18 0.00 0.54CVXNKS54 13.64 2.13 ENDO10479 95.97 4.22 ENDO28XA 39.72 8.50 ENDO8XA3.02 11.79 KID106XD 0.18 1.97 KID12XD 1.46 10.05 KID10XD 0.35 1.92KID22K 0.65 1.57 KID107XD 4.13 2.74 LNG205L 3.09 13.46 LNG315L 18.489.39 LNG507L 15.67 4.96 LNG528L 78.28 10.67 LNG8837L 14.25 6.13 LNGAC117.45 16.04 LNGAC39 151.52 5.87 LNGSQ80 27.78 24.91 LNGSQ81 9.10 5.92LVR15XA 0.27 0.09 LVR174L 0.00 0.23 LVR187L 0.00 85.59 MAM19DN 7.2118.30 MAM42DN 29.31 5.38 MAM517 13.24 1.54 MAM781M 26.05 0.95 MAM869M4.02 0.00 MAM976M 13.42 2.33 MAMS570 4.31 5.78 MAMS699 1.12 4.34 MAMS99713.01 5.21 PAN71XL 64.87 58.75 PAN77X 0.00 0.00 PAN92X 26.90 0.00 PRO10R2.57 PRO20R 5.10 PRO23B 3.74 3.66 PRO263C 3.92 PRO276P 1.99 PRO65XB 3.354.51 PRO675P 8.17 1.15 PRO767B 10.45 PRO84XB 5.75 3.97 PRO855P 3.29PRO958P 2.91 5.35 SKN287S 5.73 0.91 SKN39A 0.00 SKN669S 0.13 2.14SMINT171S 56.03 62.72 SMINT20SM 106.47 33.80 SMINTH89 96.97 40.02STO261S 118.64 19.05 STO288S 47.55 4.07 STOAC93 67.18 64.23 STO88S 79.32THRD143N 14.71 30.26 THRD270T 43.65 40.86 THRD56T 23.82 8.72 TST39X 6.895.65 TST647T 30.28 3.55 TST663T 23.55 1.69 UTR135XO 2.75 5.63 UTR85XU32.07 28.53 BLOB3 2.60 BLOB11 0.00 BLO69 0.00 BLO72 0.34 BLO73 0.00ADR48AD 0.00 BRN10BR 0.47 CLN01CL 24.82 ESO01ES 0.00 HRT46HR 0.00HUMREF00HR 4.31 KID55KD 2.28 LVR89LV 0.02 LNG90LN 10.08 MAM01MA 1.17MSL84MU 0.00 OVR3APV 0.02 PAN04PA 0.61 PLA59PL 0.00 PRO09PR 8.47 REC21RC95.94 SMINT59SM 16.37 SPL7GSP 1.00 STO09ST 2.19 THYM99TM 0.83 TRA16TR6.78 TST4GTS 1.57 UTR57UT 2.240.00 = Negative or Not Detcted

The sensitivity for Ovr232v2 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr232v2 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr232v2 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 22% 44% 67% 0% 20%  Sensitivity,Down vs. 22% 22% 22% 0% 0% NAT Sensitivity, Up vs. NRM 33% 33% 89% 92% 0% Sensitivity, Down vs.  0% 11%  0% 8% 60%  NRM Specificity 36.46%  29.28%   25.41%   24.28%    19.13%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr232v2 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr232v2 are as follows:(Ovr232v2_forward): CCTTTTTATCCACTTACAGATCAACCA (SEQ ID NO:323)(Ovr232v2_reverse): ACAAGCAAGATGCATGTGAGTGA (SEQ ID NO:324)(Ovr232v2_probe): ATGGTTCGCTGCTGCCGTT (SEQ ID NO:325)DEX0455_(—)049.nt.4 (Ovr232v3)

The relative expression level of Ovr232v3 in various tissue samples isincluded below. Tissue samples include 75 pairs of matching samples, 10non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tonormal lung sample LNG90LN (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVR084 0.00 0.00 OVRG010 0.07 0.00 OVRG021 0.00 0.00 OVR1157 0.01OVR773O 0.00 OVR988Z 0.00 OVRC360 0.00 OVR1005O 0.52 OVR1040O 0.55OVR105O 0.25 OVR130X 0.00 OVR718O 0.29 OVRA1B 0.22 OVR247A 0.00 OVRC0870.00 OVRC109 0.00 OVR206I 0.00 OVR515O 0.00 OVR18GA 0.00 OVR337O 0.00OVR123O 0.00 OVRC177 0.00 OVR40G 0.00 OVR451O 0.00 BLD030B 0.12 0.00BLD520B 0.00 0.00 BLDTR17 0.00 0.02 CLN401C 0.57 0.24 CLNAS43 1.60 0.00CLNAS98 0.86 0.00 CLNCM12 0.06 0.06 CLNDC19 0.47 0.03 CLNRC01 0.12 0.12CLNRS53 0.00 0.00 CLNSG27 1.08 0.00 CLNTX01 0.00 0.41 CVXKS52 0.00 0.00CVXNKS55 0.00 0.00 CVXNKS25 0.00 0.00 CVXNKS18 0.00 0.00 CVXNKS54 0.000.00 ENDO10479 0.30 0.00 ENDO28XA 0.19 0.00 ENDO8XA 0.00 0.46 KID106XD0.00 0.00 KID12XD 0.00 0.00 KID10XD 0.00 0.04 KID22K 0.00 0.02 KID107XD0.00 0.12 LNG205L 0.00 0.68 LNG315L 0.00 0.00 LNG507L 0.00 0.00 LNG528L1.50 0.00 LNG8837L 0.96 0.81 LNGAC11 0.03 0.00 LNGAC39 0.35 1.20 LNGSQ800.87 0.00 LNGSQ81 0.65 0.00 LVR15XA 0.10 0.00 LVR174L 0.00 0.00 LVR187L0.00 0.38 MAM19DN 0.00 0.00 MAM42DN 0.00 0.07 MAM517 0.00 0.00 MAM781M0.00 0.00 MAM869M 0.00 0.00 MAM976M 0.00 0.00 MAMS570 0.00 0.00 MAMS6990.00 0.00 MAMS997 0.05 0.21 PAN71XL 0.00 0.64 PAN77X 0.00 0.00 PAN92X0.19 0.00 PRO10R 0.00 PRO20R 0.00 PRO23B 0.04 0.00 PRO263C 0.00 PRO276P0.00 PRO65XB 0.09 0.00 PRO675P 0.68 0.00 PRO767B 0.09 PRO84XB 0.00 0.00PRO855P 0.01 PRO958P 0.00 0.00 SKN287S 0.06 0.00 SKN39A 0.00 0.00SKN669S 0.00 0.00 SMINT171S 0.03 0.00 SMINT20SM 0.55 0.24 SMINTH89 0.000.47 STO261S 1.03 0.00 STO288S 0.54 0.00 STOAC93 0.00 2.29 STO88S 0.000.00 THRD143N 0.51 2.00 THRD270T 0.49 0.97 THRD56T 0.79 0.00 TST39X 0.000.00 TST647T 0.52 0.59 TST663T 0.40 0.46 UTR135XO 0.00 0.00 UTR85XU 0.770.29 BLOB3 0.00 BLOB11 0.00 BLO69 0.00 BLO72 0.00 BLO73 0.00 ADR48AD0.00 BRN10BR 0.00 CLN01CL 0.03 CVX06CV 0.00 ESO01ES 0.00 HRT46HR 0.00HUMREF00HR 0.00 KID55KD 0.01 LVR89LV 0.00 LNG90LN 1.00 MAM01MA 0.06MSL84MU 0.00 OVR3APV 0.01 PAN04PA 0.00 PLA59PL 0.00 PRO09PR 0.00 REC21RC1.27 SMINT59SM 0.00 SPL7GSP 0.00 STO09ST 0.00 THYM99TM 0.00 TRA16TR 0.00TST4GTS 1.21 UTR57UT 0.000.00 = Negative or Not Detected

The sensitivity for Ovr232v3 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr232v3 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr232v3 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 56% 44%  0% 0% 60%  Sensitivity,Down vs. 11% 22% 22% 0% 0% NAT Sensitivity, Up vs. NRM 78%  0%  0% 62% 60%  Sensitivity, Down vs. 22% 56% 89% 0% 0% NRM Specificity 72.73%  70.59%   61.5%   62.36%    63.49%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr232v3 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr232v3 are as follows:(Ovr232v3_forward): CCTCACTTCGCAGCTTTGCT (SEQ ID NO:326)(Ovr232v3_reverse): CTGGCATTGACGATTATTATTCACA (SEQ ID NO:327)(Ovr232v3_probe): CTGTGAAAACTACAAGCTGGCCGTAAACTGCT (SEQ ID NO:328)DEX0455_(—)052.nt.2 (Ovr107v1)

The relative expression level of Ovr107v1 in various tissue samples isincluded below. Tissue samples include 69 pairs of matching samples, 14non matched cancer samples, and 33 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 2 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toprostate normal sample PRO09PR (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 1.11 0.00 OVRG010 0.00 6.59 OVRG021 0.36 0.35 OVR1157 3.79OVR773O 7.68 OVR814O 1.90 OVRC360 0.00 OVR1005O 4.09 OVR1040O 3.29OVR105O 4.05 OVR130X 0.00 OVR718O 0.84 OVRA1B 3.99 OVR247A 0.12 OVR35GA0.14 OVRC087 0.06 OVRC109 0.22 OVR206I 0.42 OVR515O 0.00 OVR18GA 0.00OVRC177 0.02 OVR40G 0.00 BLD030B 0.79 0.00 BLD520B 0.10 0.12 BLDTR172.53 1.19 CLN401C 0.26 0.44 CLNAS43 4.02 1.01 CLNAS98 1.42 0.50 CLNCM121.48 0.45 CLNDC19 2.32 0.79 CLNRC01 0.33 0.15 CLNRS53 0.31 0.88 CLNSG272.00 1.15 CLNTX01 0.00 0.00 CVXKS52 1.77 3.80 CVXNK23 1.76 CVXNKS54 2.773.22 CVXNKS55 6.45 9.73 CVXNKS81 2.00 ENDO10479 5.01 1.45 ENDO28XA 5.660.29 ENDO8XA 0.85 0.18 KID106XD 0.00 0.61 KID107XD 0.44 1.12 KID109XD2.85 0.99 KID10XD 0.00 0.09 KID22K 0.32 0.03 LNG205L 0.26 1.68 LNG315L0.44 0.44 LNG507L 0.24 0.00 LNG528L 0.19 0.17 LNG8837L 1.07 0.62 LNGAC110.63 0.30 LNGAC39 1.29 1.24 LNGSQ80 1.39 0.25 LNGSQ81 1.23 0.56 LVR15XA0.00 0.04 LVR174L 0.00 0.02 LVR187L 0.25 0.86 MAM19DN 1.91 1.04 MAM42DN0.36 0.00 MAM517 0.00 MAM781M 0.00 0.53 MAM869M 1.40 1.23 MAM976M 2.550.00 MAMS570 0.00 1.69 MAMS699 1.35 0.00 MAMS997 2.41 1.23 PAN71XL 0.720.00 PAN82XP 0.71 PAN92X 5.33 PRO23B 1.06 0.93 PRO65XB 0.61 0.70 PRO675P0.57 0.48 PRO84XB 0.62 0.75 PRO958P 1.10 1.03 PRO263C 1.38 PRO276P 0.66PRO767B 2.26 PRO855P 0.76 PRO10R 0.26 PRO20R 0.36 SKN287S 2.27 0.00SKN39A 0.54 0.00 SKN669S 0.52 6.42 SMINT171S 1.91 0.09 SMINT20SM 3.081.13 SMINTH89 1.92 1.28 STO261S 1.20 0.35 STO288S 0.14 0.29 STO88S 0.580.00 THRD143N 1.09 6.12 THRD270T 5.60 6.15 THRD56T 2.63 2.16 TST39X 0.580.29 TST647T 0.41 0.03 TST663T 0.95 0.07 UTR135XO 0.63 1.00 UTR85XU 0.000.19 BLOB3 0.35 BLOB11 0.00 ADR48AD 0.00 BRN10BR 0.00 CLN01CL 0.79ESO01ES 1.69 HRT46HR 0.00 HUMREF00HR 0.67 KID55KD 0.17 LVR89LV 0.00LNG90LN 0.36 MAM01MA 0.55 MSL84MU 0.00 OVR3APV 0.33 PAN04PA 0.24 PLA59PL5.67 PRO09PR 1.00 REC21RC 0.51 SMINT59SM 0.12 SPL7GSP 0.08 STO09ST 2.33THYM99TM 0.20 TRA16TR 2.37 TST4GTS 0.33 UTR57UT 0.32Note:0.00 = Negative or Not Detected

The sensitivity for Ovr107v1 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr107v1 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr107v1 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. NAT 56% 44% 38%  0% 0% Sensitivity, Downvs. 11% 11% 25%  0% 0% NAT Sensitivity, Up vs. NRM 33% 44% 63% 77% 0%Sensitivity, Down vs. 44%  0% 25% 23% 0% NRM Specificity 25.86%  21.26%   22.86%   25.15%   21.59%   

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr107v1 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr107v1 are as follows:(Ovr107v1_forward): CGCCTGACCCGACTGTCTTA (SEQ ID NO:329)(Ovr107v1_reverse): GCTCAGATTCTGGCTCCAAGTCT (SEQ ID NO:330)(Ovr107v1-probe): CCTACAGCAAAGCGCCCCCCA (SEQ ID NO:331)DEX0455_(—)052.nt.4 (Ovr107v3)

The relative expression level of Ovr107v3 in various tissue samples isincluded below. Tissue samples include 73 pairs of matching samples, 11non matched cancer samples, and 37 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 4 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared toovarian cancer sample OVR8140 (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample CAN NAT NRM BPH PROSTOVRA084 0.32 0.10 OVRG010 0.01 4.12 OVRG021 0.17 0.04 OVR1157 2.88OVR773O 6.48 OVR814O 1.00 OVRC360 0.11 OVR1005O 1.56 OVR1040O 1.09OVR105O 0.68 OVR130X 1.17 OVR718O 0.79 OVRA1B 1.43 OVR247A 0.06 OVR35GA0.03 OVRC087 0.03 OVRC109 0.01 OVR206I 0.08 OVR515O 0.09 OVR18GA 0.03OVR337O 0.00 OVR123O 0.00 OVRC177 0.04 OVR40G 0.05 BLD030B 0.16 0.00BLD520B 0.09 0.03 BLDTR17 0.06 0.16 CLN401C 0.09 0.10 CLNAS43 0.24 0.03CLNAS98 0.14 0.11 CLNCM12 0.05 0.11 CLNDC19 0.40 0.14 CLNRC01 0.05 0.07CLNRS53 0.06 0.16 CLNSG27 0.11 0.12 CLNTX01 0.07 0.02 CVXKS52 0.50 1.56CVXNK23 0.51 2.02 CVXNKS54 0.56 0.93 CVXNKS55 1.32 3.28 CVXNKS81 0.551.16 ENDO10479 1.12 0.12 ENDO28XA 1.33 0.11 ENDO8XA 0.30 0.07 KID106XD0.01 0.03 KID107XD 0.03 0.13 KID109XD 0.25 0.04 KID10XD 0.02 0.01 KID22K0.07 0.03 LNG205L 0.03 0.05 LNG315L 0.03 0.08 LNG507L 0.58 0.07 LNG528L0.29 0.06 LNG8837L 0.09 0.17 LNGAC11 0.14 0.15 LNGAC39 0.50 0.08 LNGSQ800.18 0.22 LNGSQ81 0.07 0.16 LVR15XA 0.00 0.01 LVR174L 0.01 0.01 LVR187L0.01 0.19 MAM19DN 0.62 0.28 MAM42DN 0.57 0.37 MAM517 2.06 0.15 MAM781M0.07 0.06 MAM869M 0.67 0.11 MAM976M 0.60 0.16 MAMS570 0.72 0.76 MAMS6990.10 0.46 MAMS997 0.18 0.34 PAN71XL 0.09 0.02 PAN82XP 0.12 PAN92X 2.580.00 PRO23B 0.23 0.27 PRO65XB 0.22 0.25 PRO675P 0.40 0.19 PRO84XB 0.340.42 PRO958P 0.38 0.22 PRO263C 0.30 PRO276P 0.24 PRO767B 0.93 PRO855P0.44 PRO10R 0.32 PRO20R 0.19 SKN287S 0.86 0.00 SKN39A 0.03 0.00 SKN669S0.12 0.40 SMINT171S 0.21 0.04 SMINT20SM 2.32 0.40 SMINTH89 0.51 0.05STO261S 0.65 0.05 STO288S 0.08 0.03 STO88S 0.15 0.07 THRD143N 0.09 0.73THRD270T 1.23 1.14 THRD56T 0.64 0.18 TST39X 0.07 0.02 TST647T 0.11 0.01TST663T 0.12 0.03 UTR135XO 0.13 0.27 UTR85XU 0.15 0.09 BLOB3 0.00 BLOB60.69 BLOB11 0.02 BLO982B 0.10 ADR48AD 0.02 BRN10BR 0.01 CLN01CL 0.05ESO01ES 0.93 HRT46HR 0.00 HUMREF00HR 0.09 KID55KD 0.05 LVR89LV 0.00LNG90LN 0.04 MAM01MA 0.15 MSL84MU 0.01 OVR3APV 0.07 PAN04PA 0.10 PLA59PL0.82 PRO09PR 0.50 REC21RC 0.26 SMINT59SM 0.03 SPL7GSP 0.03 STO09ST 1.10THYM99TM 0.02 TRA16TR 0.32 TST4GTS 0.01 UTR57UT 0.08Note:0.00 = Negative or Not Detected

The sensitivity for Ovr107v3 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr107v3 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr107v3 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, 33% 33% 44%  0% 20% Up vs. NAT Sensitivity, 22%22% 11%  0%  0% Down vs. NAT Sensitivity, 44% 67% 67% 92%  0% Up vs. NRMSensitivity,  0%  0% 11%  8% 40% Down vs. NRM Specificity 8.79%  10.44%   33.52%   43.35%   21.74%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr107v3 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr107v3 are as follows:(Ovr107v3_forward): CCTGCAGCCCAGAGCAAT (SEQ ID NO:332)(Ovr107v3_reverse): GCTCAGATTCTGGCTCCAAGTC (SEQ ID NO:333)(Ovr107v3-probe): ATCTCCAACCCTCCCGCTTCT (SEQ ID NO:334)DEX0455_(—)051.nt.6 (Ovr107v4)

The relative expression level of Ovr107v4 in various tissue samples isincluded below. Tissue samples include 69 pairs of matching samples, 15non matched cancer samples, and 34 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 2 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tobreast normal sample MAM01MA (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 1.03 0.60 OVRG010 0.43 1.15 OVRG021 0.72 1.63 OVR1157 0.00OVR773O 2.63 OVR814O 1.26 OVRC360 0.46 OVR1005O 13.92 OVR1040O 6.00OVR105O 6.04 OVR718O 4.15 OVRA1B 3.67 OVR247A 0.55 OVR35GA 1.06 OVRC0870.35 OVRC109 0.43 OVR206I 0.93 OVR515O 2.17 OVR18GA 1.17 OVRC177 0.68OVR40G 1.89 OVRC004 0.00 BLD030B 0.77 0.00 BLD520B 2.75 0.88 BLDTR170.70 2.67 CLN401C 0.78 1.03 CLNAS43 2.36 0.77 CLNAS98 1.73 1.27 CLNCM120.67 0.61 CLNDC19 1.46 0.43 CLNRC01 0.12 0.36 CLNRS53 0.36 2.08 CLNSG270.48 2.08 CLNTX01 0.72 0.56 CVXKS52 1.32 10.88 CVXNK23 2.75 CVXNKS541.33 10.06 CVXNKS55 9.56 20.77 CVXNKS81 3.27 ENDO10479 3.77 4.17ENDO28XA 5.41 4.55 ENDO8XA 1.21 1.31 KID106XD 0.27 0.12 KID107XD 0.600.45 KID109XD 2.94 0.76 KID10XD 0.18 0.28 KID22K 0.80 0.15 LNG205L 0.461.80 LNG315L 0.37 2.06 LNG507L 1.43 LNG528L 1.26 0.85 LNG8837L 0.86 1.74LNGAC11 0.77 1.37 LNGAC39 1.28 1.22 LNGSQ80 1.34 2.91 LNGSQ81 0.95 1.01LVR15XA 0.05 0.06 LVR174L 0.10 0.05 LVR187L 0.00 0.86 MAM19DN 1.31 3.79MAM42DN 1.98 3.48 MAM517 3.35 0.00 MAM781M 0.57 0.51 MAM869M 2.29 1.06MAM976M 3.78 2.13 MAMS570 2.14 3.13 MAMS699 0.58 4.99 MAMS997 2.72 1.84PAN71XL 0.76 0.24 PAN82XP 1.49 PAN92X 4.92 PRO23B 0.87 1.01 PRO65XB 0.620.72 PRO675P 1.19 2.30 PRO84XB 0.99 2.38 PRO958P 1.31 1.39 PRO263C 1.64PRO276P 0.60 PRO767B 3.10 PRO855P 0.92 PRO10R 1.33 PRO20R 2.41 SKN287S5.46 0.65 SKN39A 2.56 0.22 SKN669S 6.12 9.44 SMINT171S 1.39 0.62SMINT20SM 7.46 2.59 SMINTH89 0.97 0.16 STO261S 4.97 3.16 STO288S 0.230.40 STO88S 3.10 0.38 THRD143N 0.70 5.66 THRD270T 11.59 12.76 THRD56T4.61 1.92 TST39X 0.91 0.00 TST647T 1.42 0.29 TST663T 1.42 0.37 UTR135XO3.28 4.02 UTR85XU 1.51 2.11 BLOB3 0.25 BLOB11 0.92 ADR48AD 0.00 BRN10BR0.00 CLN01CL 0.22 ESO01ES 7.88 HRT46HR 0.06 HUMREF00HR 0.49 KID55KD 0.10LVR89LV 0.03 LNG90LN 0.26 MAM01MA 1.00 MSL84MU 0.06 OVR3APV 1.02 PAN04PA0.14 PLA59PL 2.01 PRO09PR 0.57 REC21RC 1.21 SMINT59SM 0.11 SPL7GSP 0.26STO09ST 1.56 THYM99TM 0.20 TRA16TR 1.45 TST4GTS 0.19 UTR57UT 1.280.00 = Negative or no expression

The sensitivity for Ovr107v4 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr107v4 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr107v4 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity, Up vs. 22% 0% 22%  0%  0% NAT Sensitivity, Downvs. 33% 50%  22%  0% 20% NAT Sensitivity, Up vs. 78% 78%  56% 50% 40%NRM Sensitivity, Down vs.  0% 0%  0% 25%  0% NRM Specificity 8.05%   8%13.79%   13.17%   7.95%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr107v4 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Primers used for QPCR Expression Analysis of Ovr107v4 are as follows:(Ovr107v4_forward): GGAGCCCTGAGCATTGTAATATG (SEQ ID NO:335)(Ovr107v4_reverse): CCCTGGTAGCCGGGTAGAG (SEQ ID NO:336)(Ovr107v4_probe): CAGATGGTGTGCCAACTGCTGT (SEQ ID NO:337)DEX0455_(—)053.nt.2 (Ovr110v1)

The relative expression level of Ovr110v1 in various tissue samples isincluded below. Tissue samples include 74 pairs of matching samples, 11non matched cancer samples, and 39 normal samples, all from varioustissues annotated in the table. A matching pair is formed by mRNA fromthe cancer sample for a particular tissue and mRNA from the normaladjacent sample for that same tissue from the same individual. Of thenormal samples 5 were blood samples which measured the expression levelsin blood cells. Additionally, 2 prostatitis, and 4 Benign ProstaticHyperplasia (BPH) samples are included. All the values are compared tobreast normal sample MAM01MA (calibrator).

The table below contains the relative expression level values for thesample as compared to the calibrator. The table includes the Sample ID,and expression level values for the following samples: Cancer (CAN),Normal Adjacent Tissue (NAT), Normal Tissue (NRM), Benign ProstaticHyperplasia (BPH), and Prostatitis (PROST). Sample ID CAN NAT NRM BPHPROST OVRA084 0.00 0.00 OVRG010 0.00 0.00 OVRG021 0.00 0.00 OVR1157 4.92OVR773O 4.23 OVRC360 0.00 OVR1005O 0.00 OVR1040O 0.11 OVR105O 0.00OVR130X 0.00 OVR718O 0.33 OVRA1B 0.07 OVR35GA 0.00 OVRC087 0.00 OVRC1090.00 OVR206I 0.00 OVR515O 0.00 OVR18GA 0.00 OVR337O 0.00 OVR123O 0.00OVRC177 0.00 OVR40G 0.00 OVR451O 0.00 BLD030B 0.00 0.53 BLD520B 0.000.00 BLDTR17 0.00 0.03 CLN401C 0.00 0.00 CLNAS43 0.00 0.00 CLNAS98 0.000.00 CLNCM12 0.00 0.00 CLNDC19 0.00 0.00 CLNRC01 0.00 0.00 CLNRS53 0.000.00 CLNSG27 0.00 0.00 CLNTX01 0.00 0.00 CVXKS52 0.00 0.00 CVXNKS55 0.030.00 CVXNKS25 0.00 0.29 CVXNKS18 0.00 0.00 CVXNKS54 0.00 0.00 ENDO104790.10 0.00 ENDO28XA 0.78 0.00 ENDO8XA 0.00 0.01 KID106XD 0.00 0.00KID12XD 0.01 0.15 KID10XD 0.00 0.00 KID22K 0.00 0.01 KID107XD 0.00 0.01LNG205L 0.00 0.00 LNG315L 0.00 0.00 LNG507L 0.00 0.00 LNG528L 0.00 0.00LNG8837L 0.21 0.00 LNGAC11 0.01 0.00 LNGAC39 0.00 0.00 LNGSQ80 0.00 0.00LNGSQ81 0.08 0.00 LVR15XA 0.00 0.00 LVR174L 0.00 0.00 LVR187L 0.00 0.03MAM19DN 0.36 1.23 MAM42DN 0.09 0.00 MAM517 0.00 0.00 MAM781M 0.47 0.00MAM869M 0.46 0.00 MAM976M 0.22 0.00 MAMS570 0.55 0.45 MAMS699 0.22 1.06MAMS997 0.73 0.21 PAN71XL 0.00 0.00 PAN77X 0.00 PAN92X 0.00 0.00 PRO10R0.00 PRO20R 0.00 PRO23B 0.00 0.00 PRO263C 0.00 PRO276P 0.01 PRO65XB 0.010.01 PRO675P 0.00 0.00 PRO767B 0.35 PRO84XB 0.00 0.08 PRO855P 0.00PRO958P 0.03 0.03 SKN287S 0.00 0.00 SKN39A 0.00 0.00 SKN669S 0.00 0.00SMINT171S 0.00 0.00 SMINT20SM 0.00 0.00 SMINTH89 0.00 0.00 STO261S 0.000.00 STO288S 0.00 0.00 STOAC93 0.00 0.00 STO88S 0.00 0.00 THRD143N 0.000.00 THRD270T 0.00 0.00 THRD56T 0.00 0.00 TST39X 0.84 0.00 TST647T 0.000.00 TST663T 0.04 0.00 UTR135XO 0.00 0.00 UTR85XU 0.00 0.03 BLOB3 0.00BLOB11 0.00 BLO69 0.00 BLO72 0.00 BLO73 0.00 ADR48AD 0.00 BRN10BR 0.00CLN01CL 0.00 CVX06CV 0.00 ESO01ES 0.00 HRT46HR 0.00 HUMREF00HR 0.00KID55KD 0.00 LVR89LV 0.00 LNG90LN 0.00 MAM01MA 1.00 MSL84MU 0.00 OVR3APV0.00 PAN04PA 0.00 PLA59PL 0.00 PRO09PR 0.51 REC21RC 0.00 SMINT59SM 0.00SPL7GSP 0.00 STO09ST 0.00 THYM99TM 0.00 TRA16TR 0.15 TST4GTS 0.15UTR57UT 0.000.00 = Negative or no expression

The sensitivity for Ovr110v1 expression was calculated for the cancersamples versus normal samples. The sensitivity value indicates thepercentage of cancer samples that show levels of Ovr110v1 at least 2fold higher than the normal tissue or the corresponding normal adjacentform the same patient.

This specificity is an indication of the level of ovary tissue specificexpression of the transcript compared to all the other tissue typestested in our assay. Thus, these experiments indicate Ovr110v1 beinguseful as an ovarian cancer diagnostic marker and/or therapeutic target.

Sensitivity and specificity data is reported in the table below. CLN LNGMAM OVR PRO Sensitivity,    0% 33% 56% 0%  0% Up vs. NAT Sensitivity,   0%  0% 22% 0% 20% Down vs. NAT Sensitivity,    0% 33%  0% 42%   0% Upvs. NRM Sensitivity,    0%  0% 78% 0% 100%  Down vs. NRM Specificity74.73% 76.34%   89.78%   76.27%    79.26%  

Altogether, the tissue specificity, plus the mRNA differentialexpression in the samples tested are believed to make Ovr110v1 a goodmarker for diagnosing, monitoring, staging, imaging and/or treatingovarian cancer.

Additionally, the tissue specificity, plus the mRNA differentialexpression in the samples tested may make Ovr110v1 a good marker fordiagnosing, monitoring, staging, imaging and/or treating lung cancer.

Primers used for QPCR Expression Analysis of Ovr110v1 are as follows:(Ovr110v1_forward): TCATTGGCTTTGGTATTTCAGAAG (SEQ ID NO:338)(Ovr110v1_reverse): GTTCAGGAAGCAAAGATCAATGC (SEQ ID NO:339)(Ovr110v1_probe): AGCAATGAAGGGTTTGGTTGTAGAAG (SEQ ID NO:340)Conclusions

Altogether, the high level of tissue specificity, plus the mRNAoverexpression in matched samples tested are indicative of SEQ ID NO:1-128 being a diagnostic marker and/or a therapeutic target for cancer.

Example 3 Protein Expression

The OSNA is amplified by polymerase chain reaction (PCR) and theamplified DNA fragment encoding the OSNA is subcloned in pET-21d forexpression in E. coli. In addition to the OSNA coding sequence, codonsfor two amino acids, Met-Ala, flanking the NH₂-terminus of the codingsequence of OSNA, and six histidines, flanking the COOH-terminus of thecoding sequence of OSNA, are incorporated to serve as initiatingMet/restriction site and purification tag, respectively.

An over-expressed protein band of the appropriate molecular weight maybe observed on a Coomassie blue stained polyacrylamide gel. This proteinband is confirmed by Western blot analysis using monoclonal antibodyagainst 6× Histidine tag.

Large-scale purification of OSP is achieved using cell paste generatedfrom 6-liter bacterial cultures, and purified using immobilized metalaffinity chromatography (IMAC). Soluble fractions that are separatedfrom total cell lysate were incubated with a nickel chelating resin. Thecolumn is packed and washed with five column volumes of wash buffer. OSPis eluted stepwise with various concentration imidazole buffers.

Example 4 Fusion Proteins

The human Fc portion of the IgG molecule can be PCR amplified, usingprimers that span the 5′ and 3′ ends of the sequence described below.These primers also should have convenient restriction enzyme sites thatwill facilitate cloning into an expression vector, preferably amammalian expression vector. For example, if pC4 (Accession No. 209646)is used, the human Fc portion can be ligated into the BamHI cloningsite. Note that the 3′ BamHI site should be destroyed. Next, the vectorcontaining the human Fc portion is re-restricted with BamHI, linearizingthe vector, and a polynucleotide of the present invention, isolated bythe PCR protocol described in Example 2, is ligated into this BamHIsite. Note that the polynucleotide is cloned without a stop codon,otherwise a fusion protein will not be produced. If the naturallyoccurring signal sequence is used to produce the secreted protein, pC4does not need a second signal peptide. Alternatively, if the naturallyoccurring signal sequence is not used, the vector can be modified toinclude a heterologous signal sequence. See, e.g., WO 96/34891.

Example 5 Production of an Antibody from a Polypeptide

In general, such procedures involve immunizing an animal (preferably amouse) with polypeptide or, more preferably, with a secretedpolypeptide-expressing cell. Such cells may be cultured in any suitabletissue culture medium; however, it is preferable to culture cells inEarle's modified Eagle's medium supplemented with 10% fetal bovine serum(inactivated at about 56° C.), and supplemented with about 10 g/l ofnonessential amino acids, about 1,000 U/ml of penicillin, and about 100,μg/ml of streptomycin. The splenocytes of such mice are extracted andfused with a suitable myeloma cell line. Any suitable myeloma cell linemay be employed in accordance with the present invention; however, it ispreferable to employ the parent myeloma cell line (SP20), available fromthe ATCC. After fusion, the resulting hybridoma cells are selectivelymaintained in HAT medium, and then cloned by limiting dilution asdescribed by Wands et al., Gastroenterology 80: 225-232 (1981).

The hybridoma cells obtained through such a selection are then assayedto identify clones which secrete antibodies capable of binding thepolypeptide. Alternatively, additional antibodies capable of binding tothe polypeptide can be produced in a two-step procedure usinganti-idiotypic antibodies. Such a method makes use of the fact thatantibodies are themselves antigens, and therefore, it is possible toobtain an antibody which binds to a second antibody. In accordance withthis method, protein specific antibodies are used to immunize an animal,preferably a mouse. The splenocytes of such an animal are then used toproduce hybridoma cells, and the hybridoma cells are screened toidentify clones which produce an antibody whose ability to bind to theprotein-specific antibody can be blocked by the polypeptide. Suchantibodies comprise anti-idiotypic antibodies to the protein specificantibody and can be used to immunize an animal to induce formation offurther protein-specific antibodies.

Example 6 Method of Determining Alterations in a Gene Corresponding to aPolynucleotide

RNA is isolated from individual patients or from a family of individualsthat have a phenotype of interest. cDNA is then generated from these RNAsamples using protocols known in the art. See, Sambrook (2001), supra.The cDNA is then used as a template for PCR, employing primerssurrounding regions of interest in SEQ ID NO: 1-128. Suggested PCRconditions consist of 35 cycles at 95° C. for 30 seconds; 60-120 secondsat 52-58° C.; and 60-120 seconds at 70° C., using buffer solutionsdescribed in Sidransky et al., Science 252(5006): 706-9 (1991). See alsoSidransky et al., Science 278(5340): 1054-9 (1997).

PCR products are then sequenced using primers labeled at their 5′ endwith T4 polynucleotide kinase, employing SequiTherm Polymerase.(Epicentre Technologies). The intron-exon borders of selected exons arealso determined and genomic PCR products analyzed to confirm theresults. PCR products harboring suspected mutations are then cloned andsequenced to validate the results of the direct sequencing. PCR productsis cloned into T-tailed vectors as described in Holton et al., NucleicAcids Res., 19: 1156 (1991) and sequenced with T7 polymerase (UnitedStates Biochemical). Affected individuals are identified by mutationsnot present in unaffected individuals.

Genomic rearrangements may also be determined. Genomic clones arenick-translated with digoxigenin deoxyuridine 5′ triphosphate(Boehringer Manheim), and FISH is performed as described in Johnson etal., Methods Cell Biol. 35: 73-99 (1991). Hybridization with the labeledprobe is carried out using a vast excess of human cot-1 DNA for specifichybridization to the corresponding genomic locus.

Chromosomes are counterstained with 4,6-diamino-2-phenylidole andpropidium iodide, producing a combination of C-and R-bands. Alignedimages for precise mapping are obtained using a triple-band filter set(Chroma Technology, Brattleboro, Vt.) in combination with a cooledcharge-coupled device camera (Photometrics, Tucson, Ariz.) and variableexcitation wavelength filters. Johnson (1991). Image collection,analysis and chromosomal fractional length measurements are performedusing the ISee Graphical Program System. (Inovision Corporation, Durham,N.C.) Chromosome alterations of the genomic region hybridized by theprobe are identified as insertions, deletions, and translocations. Thesealterations are used as a diagnostic marker for an associated disease.

Example 7 Method of Detecting Abnormal Levels of a Polypeptide in aBiological Sample

Antibody-sandwich ELISAs are used to detect polypeptides in a sample,preferably a biological sample. Wells of a microtiter plate are coatedwith specific antibodies, at a final concentration of 0.2 to 10 ug/ml.The antibodies are either monoclonal or polyclonal and are produced bythe method described above. The wells are blocked so that non-specificbinding of the polypeptide to the well is reduced. The coated wells arethen incubated for >2 hours at RT with a sample containing thepolypeptide. Preferably, serial dilutions of the sample should be usedto validate results. The plates are then washed three times withdeionized or distilled water to remove unbound polypeptide. Next, 50 μlof specific antibody-alkaline phosphatase conjugate, at a concentrationof 25-400 ng, is added and incubated for 2 hours at room temperature.The plates are again washed three times with deionized or distilledwater to remove unbound conjugate. 75 μl of 4-methylumbelliferylphosphate (MUP) or p-nitrophenyl phosphate (NPP) substrate solution areadded to each well and incubated 1 hour at room temperature.

The reaction is measured by a microtiter plate reader. A standard curveis prepared, using serial dilutions of a control sample, and polypeptideconcentrations are plotted on the X-axis (log scale) and fluorescence orabsorbance on the Y-axis (linear scale). The concentration of thepolypeptide in the sample is calculated using the standard curve.

Example 8 Formulating a Polypeptide

The secreted polypeptide composition will be formulated and dosed in afashion consistent with good medical practice, taking into account theclinical condition of the individual patient (especially the sideeffects of treatment with the secreted polypeptide alone), the site ofdelivery, the method of administration, the scheduling ofadministration, and other factors known to practitioners. The “effectiveamount” for purposes herein is thus determined by such considerations.

As a general proposition, the total pharmaceutically effective amount ofsecreted polypeptide administered parenterally per dose will be in therange of about 1, μg/kg/day to 10 mg/kg/day of patient body weight,although, as noted above, this will be subject to therapeuticdiscretion. More preferably, this dose is at least 0.01 mg/kg/day, andmost preferably for humans between about 0.01 and 1 mg/kg/day for thehormone. If given continuously, the secreted polypeptide is typicallyadministered at a dose rate of about 1 μg/kg/hour to about 50mg/kg/hour, either by 1-4 injections per day or by continuoussubcutaneous infusions, for example, using a mini-pump. An intravenousbag solution may also be employed. The length of treatment needed toobserve changes and the interval following treatment for responses tooccur appears to vary depending on the desired effect

Pharmaceutical compositions containing the secreted protein of theinvention are administered orally, rectally, parenterally,intracisternally, intravaginally, intraperitoneally, topically (as bypowders, ointments, gels, drops or transdermal patch), bucally, or as anoral or nasal spray. “Pharmaceutically acceptable carrier” refers to anon-toxic solid, semisolid or liquid filler, diluent, encapsulatingmaterial or formulation auxiliary of any type. The term “parenteral” asused herein refers to modes of administration which include intravenous,intramuscular, intraperitoneal, intrasternal, subcutaneous andintraarticular injection and infusion.

The secreted polypeptide is also suitably administered bysustained-release systems. Suitable examples of sustained-releasecompositions include semipermeable polymer matrices in the form ofshaped articles, e.g., films, or microcapsules. Sustained-releasematrices include polylactides (U.S. Pat. No. 3,773,919, EP 58,481, thecontents of which are hereby incorporated by reference herein in theirentirety), copolymers of L-glutamic acid and gamma-ethyl-L-glutamate(Sidman, U. et al., Biopolymers 22: 547-556 (1983)), poly(2-hydroxyethyl methacrylate) (R. Langer et al., J. Biomed. Mater. Res.15: 167-277 (1981), and R. Langer, Chem. Tech. 12: 98-105 (1982)),ethylene vinyl acetate (R. Langer et al.) or poly-D-(−)-3-hydroxybutyricacid (EP 133,988). Sustained-release compositions also includeliposomally entrapped polypeptides. Liposomes containing the secretedpolypeptide are prepared by methods known per se: D E Epstein et al.,Proc. Natl. Acad. Sci. USA 82: 3688-3692 (1985); Hwang et al., Proc.Natl. Acad. Sci. USA 77: 40304034 (1980); EP 52,322; EP 36,676; EP88,046; EP 143,949; EP 142,641; Japanese Pat. Appl. 83-118008; U.S. Pat.Nos. 4,485,045 and 4,544,545; and EP 102,324, the contents of which arehereby incorporated by reference herein in their entirety. Ordinarily,the liposomes are of the small (about 200-800 Angstroms) unilamellartype in which the lipid content is greater than about 30 mol. percentcholesterol, the selected proportion being adjusted for the optimalsecreted polypeptide therapy.

For parenteral administration, in one embodiment, the secretedpolypeptide is formulated generally by mixing it at the desired degreeof purity, in a unit dosage injectable form (solution, suspension, oremulsion), with a pharmaceutically acceptable carrier, i.e., one that isnon-toxic to recipients at the dosages and concentrations employed andis compatible with other ingredients of the formulation.

For example, the formulation preferably does not include oxidizingagents and other compounds that are known to be deleterious topolypeptides. Generally, the formulations are prepared by contacting thepolypeptide uniformly and intimately with liquid carriers or finelydivided solid carriers or both. Then, if necessary, the product isshaped into the desired formulation. Preferably, the carrier is aparenteral carrier, more preferably, a solution that is isotonic withthe blood of the recipient. Examples of such carrier vehicles includewater, saline, Ringer's solution, and dextrose solution. Non-aqueousvehicles such as fixed oils and ethyl oleate are also useful herein, aswell as liposomes.

The carrier suitably contains minor amounts of additives such assubstances that enhance isotonicity and chemical stability. Suchmaterials are non-toxic to recipients at the dosages and concentrationsemployed, and include buffers such as phosphate, citrate, succinate,acetic acid, and other organic acids or their salts; antioxidants suchas ascorbic acid; low molecular weight (less than about ten residues)polypeptides, e.g., polyarginine or tripeptides; proteins, such as serumalbumin, gelatin, or immunoglobulins; hydrophilic polymers such aspolyvinylpyrrolidone; amino acids, such as glycine, glutamic acid,aspartic acid, or arginine; monosaccharides, disaccharides, and othercarbohydrates including cellulose or its derivatives, glucose, manose,or dextrins; chelating agents such as EDTA; sugar alcohols such asmannitol or sorbitol; counterions such as sodium; and/or nonionicsurfactants such as polysorbates, poloxamers, or PEG.

The secreted polypeptide is typically formulated in such vehicles at aconcentration of about 0.1 mg/ml to 100 mg/ml, preferably 1-10 mg/ml, ata pH of about 3 to 8. It will be understood that the use of certain ofthe foregoing excipients, carriers, or stabilizers will result in theformation of polypeptide salts.

Any polypeptide to be used for therapeutic administration can besterile. Sterility is readily accomplished by filtration through sterilefiltration membranes (e.g., 0.2 micron membranes). Therapeuticpolypeptide compositions generally are placed into a container having asterile access port, for example, an intravenous solution bag or vialhaving a stopper pierceable by a hypodermic injection needle.

Polypeptides ordinarily will be stored in unit or multi-dose containers,for example, sealed ampules or vials, as an aqueous solution or as alyophilized formulation for reconstitution. As an example of alyophilized formulation, 10-ml vials are filled with 5 ml ofsterile-filtered 1% (w/v) aqueous polypeptide solution, and theresulting mixture is lyophilized. The infusion solution is prepared byreconstituting the lyophilized polypeptide using bacteriostaticWater-for-Injection.

The invention also provides a pharmaceutical pack or kit comprising oneor more containers filled with one or more of the ingredients of thepharmaceutical compositions of the invention. Associated with suchcontainer (s) can be a notice in the form prescribed by a governmentalagency regulating the manufacture, use or sale of pharmaceuticals orbiological products, which notice reflects approval by the agency ofmanufacture, use or sale for human administration. In addition, thepolypeptides of the present invention may be employed in conjunctionwith other therapeutic compounds.

Example 9 Method of Treating Decreased Levels of the Polypeptide

It will be appreciated that conditions caused by a decrease in thestandard or normal expression level of a secreted protein in anindividual can be treated by administering the polypeptide of thepresent invention, preferably in the secreted form. Thus, the inventionalso provides a method of treatment of an individual in need of anincreased level of the polypeptide comprising administering to such anindividual a pharmaceutical composition comprising an amount of thepolypeptide to increase the activity level of the polypeptide in such anindividual.

For example, a patient with decreased levels of a polypeptide receives adaily dose 0.1-100 ug/kg of the polypeptide for six consecutive days.Preferably, the polypeptide is in the secreted form. The exact detailsof the dosing scheme, based on administration and formulation, areprovided above.

Example 10 Method of Treating Increased Levels of the Polypeptide

Antisense or RNAi technology are used to inhibit production of apolypeptide of the present invention. This technology is one example ofa method of decreasing levels of a polypeptide, preferably a secretedform, due to a variety of etiologies, such as cancer.

For example, a patient diagnosed with abnormally increased levels of apolypeptide is administered intravenously antisense polynucleotides at0.5, 1.0, 1.5, 2.0 and 3.0 mg/kg day for 21 days. This treatment isrepeated after a 7-day rest period if the treatment was well tolerated.The formulation of the antisense polynucleotide is provided above.

Example 11 Method of Treatment Using Gene Therapy

One method of gene therapy transplants fibroblasts, which are capable ofexpressing a polypeptide, onto a patient. Generally, fibroblasts areobtained from a subject by skin biopsy. The resulting tissue is placedin tissue-culture medium and separated into small pieces. Small chunksof the tissue are placed on a wet surface of a tissue culture flask,approximately ten pieces are placed in each flask The flask is turnedupside down, closed tight and left at room temperature over night. After24 hours at room temperature, the flask is inverted and the chunks oftissue remain fixed to the bottom of the flask and fresh media (e.g.,Ham's F12 media, with 10% FBS, penicillin and streptomycin) is added.The flasks are then incubated at 37° C. for approximately one week.

At this time, fresh media is added and subsequently changed everyseveral days. After an additional two weeks in culture, a monolayer offibroblasts emerge. The monolayer is trypsinized and scaled into largerflasks. pMV-7 (Kirschmeier, P. T. et al., DNA, 7: 219-25 (1988)),flanked by the long terminal repeats of the Moloney murine sarcomavirus, is digested with EcoRI and HindIII and subsequently treated withcalf intestinal phosphatase. The linear vector is fractionated onagarose gel and purified, using glass beads.

The cDNA encoding a polypeptide of the present invention can beamplified using PCR primers which correspond to the 5′and 3′endsequences respectively as set forth in Example 3. Preferably, the5′primer contains an EcoRI site and the 3′primer includes a HindIIIsite. Equal quantities of the Moloney murine sarcoma virus linearbackbone and the amplified EcoRI and HindIII fragment are addedtogether, in the presence of T4 DNA ligase. The resulting mixture ismaintained under conditions appropriate for ligation of the twofragments. The ligation mixture is then used to transform bacteria HB101, which are then plated onto agar containing kanamycin for thepurpose of confirming that the vector has the gene of interest properlyinserted.

The amphotropic pA317 or GP+am12 packaging cells are grown in tissueculture to confluent density in Dulbecco's Modified Eagles Medium (DMEM)with 10% calf serum (CS), penicillin and streptomycin. The MSV vectorcontaining the gene is then added to the media and the packaging cellstransduced with the vector. The packaging cells now produce infectiousviral particles containing the gene (the packaging cells are nowreferred to as producer cells).

Fresh media is added to the transduced producer cells, and subsequently,the media is harvested from a 10 cm plate of confluent producer cells.The spent media, containing the infectious viral particles, is filteredthrough a millipore filter to remove detached producer cells and thismedia is then used to infect fibroblast cells. Media is removed from asub-confluent plate of fibroblasts and quickly replaced with the mediafrom the producer cells. This media is removed and replaced with freshmedia.

If the titer of virus is high, then virtually all fibroblasts will beinfected and no selection is required. If the titer is very low, then itis necessary to use a retroviral vector that has a selectable marker,such as neo or his. Once the fibroblasts have been efficiently infected,the fibroblasts are analyzed to determine whether protein is produced.

The engineered fibroblasts are then transplanted onto the host, eitheralone or after having been grown to confluence on cytodex 3 microcarrierbeads.

Example 12 Method of Treatment Using Gene Therapy-In Vivo

Another aspect of the present invention is using in vivo gene therapymethods to treat disorders, diseases and conditions. The gene therapymethod relates to the introduction of naked nucleic acid (DNA, RNA, andantisense DNA or RNA) sequences into an animal to increase or decreasethe expression of the polypeptide.

The polynucleotide of the present invention may be operatively linked toa promoter or any other genetic elements necessary for the expression ofthe polypeptide by the target tissue. Such gene therapy and deliverytechniques and methods are known in the art, see, for example, Tabata H.et al. Cardiovasc. Res. 35 (3): 470-479 (1997); Chao J et al. Pharmacol.Res. 35 (6): 517-522 (1997); Wolff J. A. Neuromuscul. Disord. 7 (5):314-318 (1997), Schwartz B. et al. Gene Ther. 3 (5): 405-411 (1996); andTsurumi Y. et al. Circulation 94 (12): 3281-3290 (1996); WO 90/11092, WO98/11779; U.S. Pat. No. 5,693,622; 5,705,151; 5,580,859, the contents ofwhich are hereby incorporated by reference herein in their entirety.

The polynucleotide constructs may be delivered by any method thatdelivers injectable materials to the cells of an animal, such as,injection into the interstitial space of tissues (heart, muscle, skin,ovarian, liver, intestine and the like). The polynucleotide constructscan be delivered in a pharmaceutically acceptable liquid or aqueouscarrier.

The term “naked” polynucleotide, DNA or RNA, refers to sequences thatare free from any delivery vehicle that acts to assist, promote, orfacilitate entry into the cell, including viral sequences, viralparticles, liposome formulations, lipofectin or precipitating agents andthe like. However, the polynucleotides of the present invention may alsobe delivered in liposome formulations (such as those taught in FelgnerP. L. et al. Ann. NY Acad. Sci. 772: 126-139 (1995) and Abdallah B. etal. Biol. Cell 85 (1): 1-7 (1995)) which can be prepared by methods wellknown to those skilled in the art.

The polynucleotide vector constructs used in the gene therapy method arepreferably constructs that will not integrate into the host genome norwill they contain sequences that allow for replication. Any strongpromoter known to those skilled in the art can be used for driving theexpression of DNA. Unlike other gene therapies techniques, one majoradvantage of introducing naked nucleic acid sequences into target cellsis the transitory nature of the polynucleotide synthesis in the cells.Studies have shown that non-replicating DNA sequences can be introducedinto cells to provide production of the desired polypeptide for periodsof up to six months.

The polynucleotide construct can be delivered to the interstitial spaceof tissues within the an animal, including of muscle, skin, brain,ovarian, liver, spleen, bone marrow, thymus, heart, lymph, blood, bone,cartilage, pancreas, kidney, gall bladder, stomach, intestine, testis,ovary, uterus, rectum, nervous system, eye, gland, and connectivetissue. Interstitial space of the tissues comprises the intercellularfluid, mucopolysaccharide matrix among the reticular fibers of organtissues, elastic fibers in the walls of vessels or chambers, collagenfibers of fibrous tissues, or that same matrix within connective tissueensheathing muscle cells or in the lacunae of bone. It is similarly thespace occupied by the plasma of the circulation and the lymph fluid ofthe lymphatic channels. Delivery to the interstitial space of muscletissue is preferred for the reasons discussed below. They may beconveniently delivered by injection into the tissues comprising thesecells. They are preferably delivered to and expressed in persistent,non-dividing cells which are differentiated, although delivery andexpression may be achieved in non-differentiated or less completelydifferentiated cells, such as, for example, stem cells of blood or skinfibroblasts. In vivo muscle cells are particularly competent in theirability to take up and express polynucleotides.

For the naked polynucleotide injection, an effective dosage amount ofDNA or RNA will be in the range of from about 0.05 μg/kg body weight toabout 50 mg/kg body weight Preferably the dosage will be from about0.005 mg/kg to about 20 mg/kg and more preferably from about 0.05 mg/kgto about 5 mg/kg. Of course, as the artisan of ordinary skill willappreciate, this dosage will vary according to the tissue site ofinjection. The appropriate and effective dosage of nucleic acid sequencecan readily be determined by those of ordinary skill in the art and maydepend on the condition being treated and the route of administration.The preferred route of administration is by the parenteral route ofinjection into the interstitial space of tissues. However, otherparenteral routes may also be used, such as, inhalation of an aerosolformulation particularly for delivery to ovarians or bronchial tissues,throat or mucous membranes of the nose. In addition, nakedpolynucleotide constructs can be delivered to arteries duringangioplasty by the catheter used in the procedure.

The dose response effects of injected polynucleotide in muscle in vivois determined as follows. Suitable template DNA for production of mRNAcoding for polypeptide of the present invention is prepared inaccordance with a standard recombinant DNA methodology. The templateDNA, which may be either circular or linear, is either used as naked DNAor complexed with liposomes. The quadriceps muscles of mice are theninjected with various amounts of the template DNA.

Five to six week old female and male Balb/C mice are anesthetized byintraperitoneal injection with 0.3 ml of 2.5% Avertin. A 1.5 cm incisionis made on the anterior thigh, and the quadriceps muscle is directlyvisualized. The template DNA is injected in 0.1 ml of carrier in a 1 ccsyringe through a 27 gauge needle over one minute, approximately 0.5 cmfrom the distal insertion site of the muscle into the knee and about 0.2cm deep. A suture is placed over the injection site for futurelocalization, and the skin is closed with stainless steel clips.

After an appropriate incubation time (e.g., 7 days) muscle extracts areprepared by excising the entire quadriceps. Every fifth 15 umcross-section of the individual quadriceps muscles is histochemicallystained for protein expression. A time course for protein expression maybe done in a similar fashion except that quadriceps from different miceare harvested at different times. Persistence of DNA in muscle followinginjection may be determined by Southern blot analysis after preparingtotal cellular DNA and HIRT supernatants from injected and control mice.

The results of the above experimentation in mice can be use toextrapolate proper dosages and other treatment parameters in humans andother animals using naked DNA.

Example 13 Transgenic Animals

The polypeptides of the invention can also be expressed in transgenicanimals. Animals of any species, including, but not limited to, mice,rats, rabbits, hamsters, guinea pigs, pigs, micro-pigs, goats, sheep,cows and non-human primates, e.g., baboons, monkeys, and chimpanzees maybe used to generate transgenic animals. In a specific embodiment,techniques described herein or otherwise known in the art, are used toexpress polypeptides of the invention in humans, as part of a genetherapy protocol.

Any technique known in the art may be used to introduce the transgene(I.e., polynucleotides of the invention) into animals to produce thefounder lines of transgenic animals. Such techniques include, but arenot limited to, pronuclear microinjection (Paterson et al., Appl.Microbiol. Biotechnol. 40: 691-698 (1994); Carver et al., Biotechnology11: 1263-1270 (1993); Wright et al., Biotechnology 9: 830-834 (1991);and U.S. Pat. No. 4,873,191, the contents of which is herebyincorporated by reference herein in its entirety); retrovirus mediatedgene transfer into germ lines (Van der Putten et al., Proc. Natl. Acad.Sci., USA 82: 6148-6152 (1985)), blastocysts or embryos; gene targetingin embryonic stem cells (Thompson et al., Cell 56: 313-321 (1989));electroporation of cells or embryos (Lo, 1983, Mol Cell. Biol. 3:1803-1814 (1983)); introduction of the polynucleotides of the inventionusing a gene gun (see, e.g., Ulmer et al., Science 259: 1745 (1993);introducing nucleic acid constructs into embryonic pleuripotent stemcells and transferring the stem cells back into the blastocyst; andsperm mediated gene transfer (Lavitrano et al., Cell 57: 717-723 (1989).For a review of such techniques, see Gordon, “Transgenic Animals,” Intl.Rev. Cytol. 115: 171-229 (1989).

Any technique known in the art may be used to produce transgenic clonescontaining polynucleotides of the invention, for example, nucleartransfer into enucleated oocytes of nuclei from cultured embryonic,fetal, or adult cells induced to quiescence (Campell et al., Nature 380:64-66 (1996); Wilmut et al., Nature 385: 810813 (1997)).

The present invention provides for transgenic animals that carry thetransgene in all their cells, as well as animals which carry thetransgene in some, but not all their cells, I.e., mosaic animals orchimeric. The transgene may be integrated as a single transgene or asmultiple copies such as in concatamers, e.g., head-to-head tandems orhead-to-tail tandems. The transgene may also be selectively introducedinto and activated in a particular cell type by following, for example,the teaching of Lasko et al. (Lasko et al., Proc. Natl. Acad. Sci. USA89: 6232-6236 (1992)). The regulatory sequences required for such acell-type specific activation will depend upon the particular cell typeof interest, and will be apparent to those of skill in the art. When itis desired that the polynucleotide transgene be integrated into thechromosomal site of the endogenous gene, gene targeting is preferred.Briefly, when such a technique is to be utilized, vectors containingsome nucleotide sequences homologous to the endogenous gene are designedfor the purpose of integrating, via homologous recombination withchromosomal sequences, into and disrupting the function of thenucleotide sequence of the endogenous gene. The transgene may also beselectively introduced into a particular cell type, thus inactivatingthe endogenous gene in only that cell type, by following, for example,the teaching of Gu et al. (Gu et al., Science 265: 103-106 (1994)). Theregulatory sequences required for such a cell-type specific inactivationwill depend upon the particular cell type of interest, and will beapparent to those of skill in the art.

Once transgenic animals have been generated, the expression of therecombinant gene may be assayed utilizing standard techniques. Initialscreening may be accomplished by Southern blot analysis or PCRtechniques to analyze animal tissues to verify that integration of thetransgene has taken place. The level of mRNA expression of the transgenein the tissues of the transgenic animals may also be assessed usingtechniques which include, but are not limited to, Northern blot analysisof tissue samples obtained from the animal, in situ hybridizationanalysis, and reverse transcriptase-PCR (rt-PCR). Samples of transgenicgene-expressing tissue may also be evaluated immunocytochemically orimmunohistochemically using antibodies specific for the transgeneproduct.

Once the founder animals are produced, they may be bred, inbred,outbred, or crossbred to produce colonies of the particular animal.Examples of such breeding strategies include, but are not limited to:outbreeding of founder animals with more than one integration site inorder to establish separate lines; inbreeding of separate lines in orderto produce compound transgenics that express the transgene at higherlevels because of the effects of additive expression of each transgene;crossing of heterozygous transgenic animals to produce animalshomozygous for a given integration site in order to both augmentexpression and eliminate the need for screening of animals by DNAanalysis; crossing of separate homozygous lines to produce compoundheterozygous or homozygous lines; and breeding to place the transgene ona distinct background that is appropriate for an experimental model ofinterest

Transgenic animals of the invention have uses which include, but are notlimited to, animal model systems useful in elaborating the biologicalfunction of polypeptides of the present invention, studying conditionsand/or disorders associated with aberrant expression, and in screeningfor compounds effective in ameliorating such conditions and/ordisorders.

Example 14 Knock-Out Animals

Endogenous gene expression can also be reduced by inactivating or“knocking out” the gene and/or its promoter using targeted homologousrecombination. (E.g., see Smithies et al., Nature 317: 230-234 (1985);Thomas & Capecchi, Cell 51: 503512 (1987); Thompson et al., Cell 5:313-321 (1989)) Alternatively, RNAi technology may be used. For example,a mutant, non-functional polynucleotide of the invention (or acompletely unrelated DNA sequence) flanked by DNA homologous to theendogenous polynucleotide sequence (either the coding regions orregulatory regions of the gene) can be used, with or without aselectable marker and/or a negative selectable marker, to transfectcells that express polypeptides of the invention in vivo. In anotherembodiment, techniques known in the art are used to generate knockoutsin cells that contain, but do not express the gene of interest.Insertion of the DNA construct, via targeted homologous recombination,results in inactivation of the targeted gene. Such approaches areparticularly suited in research and agricultural fields wheremodifications to embryonic stem cells can be used to generate animaloffspring with an inactive targeted gene (e.g., see Thomas & Capecchi1987 and Thompson 1989, supra). However, this approach can be routinelyadapted for use in humans provided the recombinant DNA constructs aredirectly administered or targeted to the required site in vivo usingappropriate viral vectors that will be apparent to those of skill in theart.

In further embodiments of the invention, cells that are geneticallyengineered to express the polypeptides of the invention, oralternatively, that are genetically engineered not to express thepolypeptides of the invention (e.g., knockouts) are administered to apatient in vivo. Such cells may be obtained from the patient (i.e.,animal, including human) or an MHC compatible donor and can include, butare not limited to fibroblasts, bone marrow cells, blood cells (e.g.,lymphocytes), adipocytes, muscle cells, endothelial cells etc. The cellsare genetically engineered in vitro using recombinant DNA techniques tointroduce the coding sequence of polypeptides of the invention into thecells, or alternatively, to disrupt the coding sequence and/orendogenous regulatory sequence associated with the polypeptides of theinvention, e.g., by transduction (using viral vectors, and preferablyvectors that integrate the transgene into the cell genome) ortransfection procedures, including, but not limited to, the use ofplasmids, cosmids, YACs, naked DNA, electroporation, liposomes, etc.

The coding sequence of the polypeptides of the invention can be placedunder the control of a strong constitutive or inducible promoter orpromoter/enhancer to achieve expression, and preferably secretion, ofthe polypeptides of the invention. The engineered cells which expressand preferably secrete the polypeptides of the invention can beintroduced into the patient systemically, e.g., in the circulation, orintraperitoneally.

Alternatively, the cells can be incorporated into a matrix and implantedin the body, e.g., genetically engineered fibroblasts can be implantedas part of a skin graft; genetically engineered endothelial cells can beimplanted as part of a lymphatic or vascular graft. (See, for example,Anderson et al. U.S. Pat. No. 5,399,349; and Mulligan & Wilson, U.S.Pat. No. 5,460,959, the contents of which are hereby incorporated byreference herein in their entirety).

When the cells to be administered are non-autologous or non-MHCcompatible cells, they can be administered using well known techniqueswhich prevent the development of a host immune response against theintroduced cells. For example, the cells may be introduced in anencapsulated form which, while allowing for an exchange of componentswith the immediate extracellular environment, does not allow theintroduced cells to be recognized by the host immune system.

Transgenic and “knock-out” animals of the invention have uses whichinclude, but are not limited to, animal model systems useful inelaborating the biological function of polypeptides of the presentinvention, studying conditions and/or disorders associated with aberrantexpression, and in screening for compounds effective in amelioratingsuch conditions and/or disorders.

While preferred illustrative embodiments of the present invention aredescribed, one skilled in the art will appreciate that the presentinvention can be practiced by other than the described embodiments,which are presented for purposes of illustration only and not by way oflimitation. The present invention is limited only by the claims thatfollow.

1. An isolated nucleic acid molecule comprising: (a) a nucleic acidmolecule comprising a nucleic acid sequence that encodes an amino acidsequence of SEQ ID NO: 129-295; (b) a nucleic acid molecule comprising anucleic acid sequence of SEQ ID NO: 1-128; (c) a nucleic acid moleculethat selectively hybridizes to the nucleic acid molecule of (a) or (b);or (d) a nucleic acid molecule having at least 95% sequence identity tothe nucleic acid molecule of (a) or (b).
 2. The nucleic acid moleculeaccording to claim 1, wherein the nucleic acid molecule is a cDNA. 3.The nucleic acid molecule according to claim 1, wherein the nucleic acidmolecule is genomic DNA.
 4. The nucleic acid molecule according to claim1, wherein the nucleic acid molecule is an RNA.
 5. The nucleic acidmolecule according to claim 1, wherein the nucleic acid molecule is amammalian nucleic acid molecule.
 6. The nucleic acid molecule accordingto claim 5, wherein the nucleic acid molecule is a human nucleic acidmolecule.
 7. A method for determining the presence of a ovarian specificnucleic acid (OSNA) in a sample, comprising the steps of: (a) contactingthe sample with the nucleic acid molecule of claim 1 under conditions inwhich the nucleic acid molecule will selectively hybridize to an ovarianspecific nucleic acid; and (b) detecting hybridization of the nucleicacid molecule to an OSNA in the sample, wherein the detection of thehybridization indicates the presence of an OSNA in the sample.
 8. Avector comprising the nucleic acid molecule of claim
 1. 9. A host cellcomprising the vector according to claim
 8. 10. A method for producing apolypeptide encoded by the nucleic acid molecule according to claim 1,comprising the steps of: (a) providing a host cell comprising thenucleic acid molecule operably linked to one or more expression controlsequences, and (b) incubating the host cell under conditions in whichthe polypeptide is produced.
 11. A polypeptide encoded by the nucleicacid molecule according to claim
 1. 12. An isolated polypeptide selectedfrom the group consisting of: (a) a polypeptide comprising an amino acidsequence with at least 95% sequence identity to of SEQ ID NO: 129-295;or (b) a polypeptide comprising an amino-acid sequence encoded by anucleic acid molecule having at least 95% sequence identity to a nucleicacid molecule comprising a nucleic acid sequence of SEQ ID NO: 1-128.13. An antibody or fragment thereof that specifically binds to apolypeptide of claim
 12. 14. A method for determining the presence of anovarian specific protein in a sample, comprising the steps of: (a)contacting the sample with a suitable reagent under conditions in whichthe reagent will selectively interact with the ovarian specific proteincomprising a polypeptide of claim 12; and (b) detecting the interactionof the reagent with an ovarian specific protein in the sample, whereinthe detection of binding indicates the presence of an ovarian specificprotein in the sample.
 15. A method for diagnosing or monitoring thepresence and metastases of ovarian cancer in a patient, comprising thesteps of: (a) determining an amount of: (i) a nucleic acid moleculecomprising a nucleic acid sequence that encodes an amino acid sequenceof SEQ ID NO: 129-295; (ii) a nucleic acid molecule comprising a nucleicacid sequence of SEQ ID NO: 1-128; (iii) a nucleic acid molecule thatselectively hybridizes to the nucleic acid molecule of (i) or (ii); (iv)a nucleic acid molecule having at least 95% sequence identity to thenucleic acid molecule of (i) or (ii); (v) a polypeptide comprising anamino acid sequence with at least 95% sequence identity to of SEQ ID NO:129-295; or (vi) a polypeptide comprising an amino acid sequence encodedby a nucleic acid molecule having at least 95% sequence identity to anucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO:1-128 and; (b) comparing the amount of the determined nucleic acidmolecule or the polypeptide in the sample of the patient to the amountof the ovarian specific marker in a normal control; wherein a differencein the amount of the nucleic acid molecule or the polypeptide in thesample compared to the amount of the nucleic acid molecule or thepolypeptide in the normal control is associated with the presence ofovarian cancer.
 16. A kit for detecting a risk of cancer or presence ofcancer in a patient, said kit comprising a means for determining thepresence of: (a) a nucleic acid molecule comprising a nucleic acidsequence that encodes an amino acid sequence of SEQ ID NO: 129-295; (b)a nucleic acid molecule comprising a nucleic acid sequence of SEQ ID NO:1-128; (c) a nucleic acid molecule that selectively hybridizes to thenucleic acid molecule of (a) or (b); or (d) a nucleic acid moleculehaving at least 95% sequence identity to the nucleic acid molecule of(a) or (b); or (e) a polypeptide of claim
 12. 17. A method of treating apatient with ovarian cancer, comprising the step of administering acomposition consisting of: (a) a nucleic acid molecule comprising anucleic acid sequence that encodes an amino acid sequence of SEQ ID NO:129-295; (b) a nucleic acid molecule comprising a nucleic acid sequenceof SEQ ID NO: 1-128; (c) a nucleic acid molecule that selectivelyhybridizes to the nucleic acid molecule of (a) or (b); (d) a nucleicacid molecule having at least 95% sequence identity to the nucleic acidmolecule of (a) or (b); or (e) a polypeptide of claim 12; to a patientin need thereof, wherein said administration induces an immune responseagainst the ovarian cancer cell expressing the nucleic acid molecule orpolypeptide.
 18. A vaccine comprising the polypeptide or the nucleicacid encoding the polypeptide of claim 12.